22 Milo: Differential Abundance

Changes in gene expression are only part of the story. In many studies, the more important biological signal is that certain cell states become more or less abundant across conditions, donors, or time points.

sclet provides a state-aware interface to miloR for cell neighbourhood differential abundance (DA) analysis. The Milo functionality in sclet is an optional dependency: you need to install miloR to run the examples. In the GitHub Actions bookdown workflow, these chunks are executed when the required packages are available, so this chapter also acts as a regression check for the DA integration layer.

22.1 Requirements

Before running Milo DA, prepare a SingleCellExperiment with:

reducedDims(sce)$PCA
colData(sce) containing a sample column and a condition column

UMAP is optional (used for visualization only).

22.2 Two-group DA (GLM)

# `conflicted` is attached by the setup chunk and `scater` brings a third
# `intersect` into the session, so the attach order below would fail without
# naming one. Same choice the setup chunk makes.
suppressMessages(library(MouseThymusAgeing))
suppressMessages(library(scater))
conflicted::conflicts_prefer(base::intersect, .quiet = TRUE)
library(sclet)

sce <- MouseSMARTseqData()
colData(sce)$Sample <- paste(colData(sce)$SortDay, colData(sce)$Age, sep = "_")

sce <- NormalizeData(sce)
sce <- RunPCA(sce)
sce <- RunUMAP(sce)

res <- RunMilo(
  sce = sce,
  sample_col = "Sample",
  condition_col = "Age",
  name = "milo_main",
  contrasts = c("Age1wk - Age4wk"),
  k1 = 11, k2 = 11, d1 = 40, d2 = 40, prop = 0.2
)

da <- res$da_results
table(da$SpatialFDR < 0.1)

## 
## FALSE  TRUE 
##   325    20

head(da)

##        logFC   logCPM         F     PValue       FDR Nhood
## 1  0.8854248 13.75617 0.4875157 0.48506113 0.7893684     1
## 2 -2.0182655 13.53681 2.1247557 0.14498140 0.4033757     2
## 3 -0.6804019 13.51842 0.2812763 0.59588294 0.8861190     3
## 4 -2.7945200 13.62681 4.0973461 0.04298904 0.2222891     4
## 5 -3.2774410 13.71092 5.3069395 0.02127022 0.1528797     5
## 6 -2.2143078 13.67219 2.4992158 0.11394884 0.3669743     6
##   SpatialFDR        contrast PValue_adj_withinNhood
## 1  0.7884234 Age1wk - Age4wk             0.48506113
## 2  0.4027576 Age1wk - Age4wk             0.14498140
## 3  0.8790454 Age1wk - Age4wk             0.59588294
## 4  0.2215557 Age1wk - Age4wk             0.04298904
## 5  0.1607883 Age1wk - Age4wk             0.02127022
## 6  0.3544729 Age1wk - Age4wk             0.11394884

get_milo(res$sce)

## $id
## [1] "milo_main"
## 
## $type
## [1] "milo"
## 
## $status
## [1] "completed"
## 
## $method
## [1] "miloR"
## 
## $inputs
## $inputs$reduction
## [1] "PCA"
## 
## $inputs$sample_col
## [1] "Sample"
## 
## $inputs$condition_col
## [1] "Age"
## 
## $inputs$covariates
## NULL
## 
## 
## $artifacts
## $artifacts$analysis_key
## [1] "milo"
## 
## $artifacts$da_results
##            logFC   logCPM            F       PValue
## 1    0.885424822 13.75617 4.875157e-01 0.4850611329
## 2   -2.018265469 13.53681 2.124756e+00 0.1449813962
## 3   -0.680401872 13.51842 2.812763e-01 0.5958829418
## 4   -2.794520000 13.62681 4.097346e+00 0.0429890352
## 5   -3.277441011 13.71092 5.306940e+00 0.0212702168
## 6   -2.214307812 13.67219 2.499216e+00 0.1139488410
## 7    1.412216917 14.07307 9.733557e-01 0.3238792907
## 8   -1.919662609 13.76313 2.041661e+00 0.1530877495
## 9    0.303862651 13.48961 5.601722e-02 0.9841738976
## 10  -4.163369017 13.53267 8.108558e+00 0.0044186929
## 11   0.149068083 13.87199 1.367748e-02 0.9069024878
## 12  -1.417661379 13.59763 1.146917e+00 0.2842328324
## 13  -1.241263608 13.66324 1.283859e+00 0.2572220424
## 14  -0.800870659 13.54175 3.929251e-01 0.5307865730
## 15  -1.477094427 14.02593 1.096520e+00 0.2950678547
## 16   0.000000000 13.89199 0.000000e+00 1.0000000000
## 17  -0.341245797 13.94449 6.446325e-02 0.7995833597
## 18  -1.304968439 13.60053 1.341808e+00 0.2467555115
## 19   1.854603060 13.64907 2.009981e+00 0.1563124305
## 20   2.855523682 13.79009 4.215366e+00 0.0400970510
## 21   3.667647023 13.64408 6.462310e+00 0.0110403050
## 22  -1.305051937 13.48726 1.427080e+00 0.2409764063
## 23  -1.175998323 13.51276 7.321751e-01 0.3922087813
## 24   3.422555109 13.55506 5.885783e+00 0.0152890694
## 25  -3.004123564 13.79703 4.265605e+00 0.0389286509
## 26  -3.238732140 13.56568 5.369028e+00 0.0205265195
## 27  -1.762332117 13.67659 1.601210e+00 0.2057745727
## 28  -0.914347458 13.71745 5.220263e-01 0.4700030900
## 29  -0.700049973 13.60289 2.985619e-01 0.5848030831
## 30  -0.102780014 13.46814 2.963816e-03 0.9565854380
## 31  -1.856863492 13.55759 1.926570e+00 0.1651790616
## 32  -0.792178552 13.77979 3.502283e-01 0.5540032980
## 33   1.043488590 13.81281 5.603868e-01 0.4541299330
## 34   1.421804051 13.74048 1.225692e+00 0.2682850402
## 35  -0.779613194 13.60202 3.343938e-01 0.5631021139
## 36  -1.982719493 13.57723 2.457559e+00 0.1170062904
## 37  -2.379832547 13.89351 2.728645e+00 0.0986083837
## 38  -0.839877411 13.63339 4.113995e-01 0.5212813073
## 39  -2.001479708 14.08909 2.106330e+00 0.1467362590
## 40   0.758255752 13.98112 3.142288e-01 0.5751149500
## 41  -1.571745503 13.79242 1.326705e+00 0.2494321188
## 42   0.679216775 13.61177 2.618692e-01 0.6088552483
## 43  -1.463258088 13.48614 1.273523e+00 0.2591459898
## 44   0.252824719 13.51225 3.584468e-02 0.8498421703
## 45  -4.320826668 13.71054 8.495884e+00 0.0035709546
## 46  -3.183865724 13.85191 4.751030e+00 0.0293144552
## 47   0.000000000 13.59009 0.000000e+00 1.0000000000
## 48  -1.334006319 13.55422 1.383015e+00 0.2409764078
## 49  -1.241921076 13.51946 1.318770e+00 0.2508526933
## 50   0.215604831 13.90014 2.612738e-02 0.8715943487
## 51  -3.077740060 13.44087 5.636038e+00 0.0176221369
## 52  -1.951385086 13.73986 2.144551e+00 0.1431224460
## 53  -1.147715276 13.72261 7.188922e-01 0.3965369305
## 54   0.565139176 13.69195 1.968212e-01 0.6573129098
## 55   0.025625707 13.46227 2.755268e-04 0.9867570025
## 56  -1.377560775 13.65057 1.390343e+00 0.2409764103
## 57  -0.742806575 13.54830 3.103903e-01 0.5774588540
## 58   1.673190738 13.49255 1.705884e+00 0.1915638082
## 59  -0.721512970 13.97977 2.560419e-01 0.6128687161
## 60  -0.102440929 13.83440 5.658770e-03 0.9400380380
## 61  -0.240940009 13.50987 3.498250e-02 0.9829060358
## 62   1.987818675 14.05491 2.171885e+00 0.1405994542
## 63  -0.752324723 13.50569 2.971059e-01 0.5857200898
## 64  -2.035747296 13.49891 2.605868e+00 0.1065145814
## 65  -4.300603668 13.77710 8.145330e+00 0.0043300806
## 66   0.000000000 13.91367 0.000000e+00 1.0000000000
## 67  -0.548711573 13.99420 1.574560e-01 0.6915218824
## 68  -3.585523463 13.64163 6.213189e+00 0.0127034726
## 69  -3.031826038 13.54386 4.799212e+00 0.0285061004
## 70  -0.948907364 13.54466 5.298987e-01 0.4666741338
## 71  -1.304811076 13.77313 1.327199e+00 0.2493440054
## 72   2.685374425 13.57864 3.934503e+00 0.0473446891
## 73  -3.849831580 13.40340 8.905627e+00 0.0028528939
## 74  -0.933311496 13.62159 4.899089e-01 0.4839915537
## 75   0.000000000 13.53805 0.000000e+00 1.0000000000
## 76  -4.045974371 13.82262 7.148026e+00 0.0075223258
## 77   0.000000000 13.60593 0.000000e+00 1.0000000000
## 78  -2.100034910 13.86716 2.300195e+00 0.1294035773
## 79  -2.495643796 13.67977 3.308622e+00 0.0689605771
## 80  -2.624336170 13.54898 3.748649e+00 0.0528909996
## 81  -1.986382217 13.93834 2.279185e+00 0.1311665641
## 82  -1.241150128 13.61480 1.284355e+00 0.2571302364
## 83  -0.424733731 13.87605 1.022713e-01 0.7491305370
## 84  -4.240984741 13.69723 8.170335e+00 0.0042708590
## 85   0.000000000 13.63254 0.000000e+00 1.0000000000
## 86  -1.988867260 13.55974 2.472706e+00 0.1158842143
## 87   0.000000000 13.55970 0.000000e+00 1.0000000000
## 88  -0.031874842 13.56901 7.009426e-04 0.9788789831
## 89   0.000000000 13.65593 0.000000e+00 1.0000000000
## 90  -2.897796502 13.65586 4.176598e+00 0.0410237980
## 91   1.315171756 13.67168 1.047648e+00 0.3060852990
## 92   0.598586922 13.69539 2.198170e-01 0.6391942133
## 93   1.937628585 13.56608 2.174145e+00 0.1403931487
## 94  -0.360680103 13.52094 7.617479e-02 0.7825580168
## 95  -1.380275025 13.78959 1.373120e+00 0.2413169209
## 96   3.308718755 13.54830 5.493425e+00 0.0191163382
## 97  -2.441129567 13.77116 3.279979e+00 0.0701733070
## 98   0.211888258 13.97664 2.481721e-02 0.8748280008
## 99   4.388656307 13.45580 9.958459e+00 0.0016080060
## 100 -1.240311757 13.58134 9.370453e-01 0.3330727919
## 101  2.013257274 13.65756 2.324846e+00 0.1273686104
## 102 -3.688399895 13.76676 6.390913e+00 0.0114927245
## 103 -1.552145316 13.73068 1.327979e+00 0.2492049891
## 104  1.831006755 13.83926 1.804596e+00 0.1792019824
## 105  0.000000000 13.62709 0.000000e+00 1.0000000000
## 106  0.000000000 13.51930 0.000000e+00 1.0000000000
## 107 -2.040587860 13.90014 2.087084e+00 0.1485948292
## 108 -0.147971079 13.69806 5.595468e-03 0.9403737342
## 109 -2.197754042 13.43310 2.954425e+00 0.0856876040
## 110  0.835852085 13.57778 4.291705e-01 0.5124180903
## 111 -2.192286773 13.63172 2.462781e+00 0.1166180759
## 112 -1.822765087 13.67895 1.794377e+00 0.1804378554
## 113 -3.830278349 13.52243 7.134281e+00 0.0075801416
## 114 -0.234900508 13.78030 3.167556e-02 0.8587468293
## 115 -0.135775402 13.58561 7.242130e-03 0.9321837993
## 116  1.622567813 13.71061 1.604612e+00 0.2052935815
## 117 -0.306671698 13.79093 5.592966e-02 0.8130559691
## 118 -1.840940652 13.65552 1.733941e+00 0.1879521610
## 119 -3.452729507 13.42683 7.036080e+00 0.0080066531
## 120  0.000000000 13.65973 0.000000e+00 1.0000000000
## 121 -2.297352819 13.41079 3.413692e+00 0.0647004127
## 122  3.289979787 13.52283 5.525241e+00 0.0187720218
## 123 -2.068398622 13.64671 2.186089e+00 0.1393081611
## 124 -1.558453425 13.47198 1.474528e+00 0.2246742265
## 125  0.690808957 13.82821 2.764886e-01 0.5990288826
## 126 -1.725395418 13.62946 1.685832e+00 0.1941947508
## 127 -1.617047494 13.68197 1.475944e+00 0.2244517583
## 128  2.559284043 13.57871 3.525173e+00 0.0604856499
## 129  3.908545191 13.66629 7.230287e+00 0.0071856010
## 130 -3.027680060 13.47966 5.123044e+00 0.0236410907
## 131  0.000000000 13.58891 0.000000e+00 1.0000000000
## 132  0.301201051 13.45652 6.417709e-02 0.8000192392
## 133 -1.781912296 13.59513 1.652044e+00 0.1987241465
## 134  0.000000000 13.80269 0.000000e+00 1.0000000000
## 135  0.394228216 13.49922 1.023834e-01 0.7489977090
## 136 -1.050922316 13.48703 6.532572e-01 0.4189784128
## 137  0.000000000 13.89323 0.000000e+00 1.0000000000
## 138  0.000000000 13.76222 0.000000e+00 1.0000000000
## 139 -0.055864084 13.49769 1.230787e-03 0.9720149076
## 140  1.283420171 13.83663 8.972883e-01 0.3435430274
## 141 -4.565326484 13.79663 8.827206e+00 0.0029779565
## 142  1.357016770 13.43876 1.257578e+00 0.2621490683
## 143 -2.713571695 13.67433 3.935343e+00 0.0473210512
## 144 -2.310610835 13.54833 2.758455e+00 0.0967870326
## 145  0.000000000 13.59432 0.000000e+00 1.0000000000
## 146 -0.312156604 13.80472 5.776676e-02 0.8100682659
## 147  2.021989295 13.51724 2.296649e+00 0.1296992633
## 148 -3.785907007 13.65389 6.783532e+00 0.0092199968
## 149  0.608258860 13.78649 2.150140e-01 0.6428802028
## 150 -3.607023633 13.75473 6.261522e+00 0.0123617711
## 151 -0.405510230 13.85345 9.185165e-02 0.7618453635
## 152 -2.383338023 13.90265 2.613945e+00 0.1059736593
## 153  3.646978944 13.59254 6.481757e+00 0.0109202758
## 154 -1.326232954 13.55072 9.850196e-01 0.3209974721
## 155 -4.153926776 13.71025 7.937815e+00 0.0048549883
## 156  0.684271547 13.67429 2.928731e-01 0.5884026980
## 157  3.796910002 13.70046 6.937246e+00 0.0084607404
## 158 -3.324950522 13.51119 5.653909e+00 0.0174435850
## 159 -1.117689834 13.73135 7.680266e-01 0.3808587272
## 160 -2.460076423 13.50311 3.207337e+00 0.0733525423
## 161  0.000000000 13.79861 0.000000e+00 1.0000000000
## 162 -2.533502308 13.59567 3.496282e+00 0.0615490827
## 163 -0.086708216 13.90094 4.182867e-03 0.9484345694
## 164  0.521949601 13.78630 1.657704e-01 0.6839111355
## 165  0.000000000 13.62406 0.000000e+00 1.0000000000
## 166 -1.724595239 13.61907 1.531664e+00 0.2159050463
## 167 -1.102197181 13.62533 6.539749e-01 0.4187230121
## 168 -0.067182403 13.86953 2.423544e-03 0.9607378208
## 169 -0.815303321 13.47153 4.244573e-01 0.5147429673
## 170  0.000000000 13.57301 0.000000e+00 1.0000000000
## 171  0.640582114 13.58090 2.550004e-01 0.6135920462
## 172 -1.986385739 13.94008 2.278563e+00 0.1312191234
## 173 -2.215428571 13.75451 2.499770e+00 0.1139087425
## 174 -3.436770957 13.73053 5.791268e+00 0.0161320823
## 175  0.000000000 13.92923 0.000000e+00 1.0000000000
## 176  5.106878746 13.66080 1.109463e+01 0.0008703279
## 177 -1.975919602 13.88505 2.294974e+00 0.1298392078
## 178 -3.992028927 13.69389 7.370065e+00 0.0066483491
## 179  0.000000000 13.65756 0.000000e+00 1.0000000000
## 180  4.746238721 13.54062 1.017398e+01 0.0014307364
## 181  0.000000000 13.78153 0.000000e+00 1.0000000000
## 182 -4.924904678 13.64799 1.045259e+01 0.0012305354
## 183 -1.377929486 13.73148 1.409054e+00 0.2409764103
## 184 -1.105484722 13.48081 7.306970e-01 0.3926870259
## 185 -0.598251091 13.50859 2.292508e-01 0.6320950688
## 186  0.000000000 13.86143 0.000000e+00 1.0000000000
## 187 -1.233110115 13.49753 8.901112e-01 0.3454802153
## 188 -2.996104097 13.52582 4.742896e+00 0.0294532578
## 189  1.164021809 13.62398 7.932183e-01 0.3731598196
## 190 -0.519297472 13.63865 1.579032e-01 0.6911066527
## 191 -2.437052553 13.58491 3.360423e+00 0.0668239729
## 192 -1.305025109 13.52042 1.367252e+00 0.2423250385
## 193  1.154428788 13.58588 8.112453e-01 0.3677837735
## 194 -1.927116197 13.41710 2.867931e+00 0.0972697908
## 195  1.315080114 13.86898 1.310255e+00 0.2523882369
## 196 -1.030192922 13.56836 5.885206e-01 0.4430180246
## 197 -1.975720692 13.97984 2.254947e+00 0.1332337422
## 198 -3.031776305 13.56612 4.808829e+00 0.0283475510
## 199  0.538731817 13.90752 1.609545e-01 0.6882916365
## 200  0.364001580 13.39565 1.060723e-01 0.7446707638
## 201  0.745155840 13.90910 3.127139e-01 0.5760377163
## 202  3.267488783 13.53763 5.378423e+00 0.0204163551
## 203 -1.263061647 13.66312 8.795806e-01 0.3483493933
## 204 -1.657289323 13.91155 1.448105e+00 0.2288735246
## 205  2.351922203 13.56864 3.047035e+00 0.0809291884
## 206  3.758888285 13.52925 6.873018e+00 0.0087698840
## 207 -1.439751071 13.54484 1.231468e+00 0.2671604337
## 208 -0.089599429 13.70455 5.148619e-03 0.9427998597
## 209 -1.635915329 13.52421 1.377144e+00 0.2406286738
## 210 -2.387953114 13.82011 3.111984e+00 0.0777624918
## 211  0.041335485 13.63596 8.622320e-04 0.9765753039
## 212 -2.764357468 13.49882 4.052907e+00 0.0441341204
## 213 -0.383286739 13.51674 8.797057e-02 0.7773748831
## 214  0.000000000 13.49840 0.000000e+00 1.0000000000
## 215 -3.600433258 13.71138 6.307027e+00 0.0120486934
## 216 -2.238601368 13.56206 2.768744e+00 0.0961669865
## 217 -0.463465303 13.55235 1.365483e-01 0.7117482350
## 218 -0.781319138 13.95224 3.389713e-01 0.5604426076
## 219  0.000000000 13.60255 0.000000e+00 1.0000000000
## 220 -1.305049521 13.49029 1.419345e+00 0.2409764063
## 221  0.000000000 13.92522 0.000000e+00 1.0000000000
## 222  0.000000000 13.78243 0.000000e+00 1.0000000000
## 223  2.249336570 13.54555 2.748658e+00 0.0973815214
## 224 -0.606020700 13.76468 2.075452e-01 0.6487126537
## 225  0.000000000 13.85252 0.000000e+00 1.0000000000
## 226 -2.745457546 13.59314 4.055379e+00 0.0440695793
## 227 -0.618021628 13.55162 2.328065e-01 0.6294659395
## 228 -2.246942342 13.87080 2.547728e+00 0.1104987700
## 229 -3.437994667 13.68626 5.743127e+00 0.0165797539
## 230  0.000000000 14.01469 0.000000e+00 1.0000000000
## 231  0.000000000 13.65001 0.000000e+00 1.0000000000
## 232 -1.189457284 13.86645 7.021617e-01 0.4020873010
## 233  4.469027665 13.49421 9.615930e+00 0.0019367466
## 234 -2.487963054 13.63363 3.393378e+00 0.0655016108
## 235  1.262268189 13.78591 9.295969e-01 0.3350014933
## 236 -2.095733702 13.55419 2.608533e+00 0.1063357997
## 237 -0.654132139 13.54633 2.470895e-01 0.6191477633
## 238 -3.301309239 13.50814 5.619642e+00 0.0177875957
## 239  0.000000000 13.45486 0.000000e+00 1.0000000000
## 240  0.000000000 13.65827 0.000000e+00 1.0000000000
## 241  0.000000000 13.80428 0.000000e+00 1.0000000000
## 242 -2.096071108 13.71734 2.585348e+00 0.1079024396
## 243  4.869979717 13.57244 1.055788e+01 0.0011624817
## 244 -2.353325111 13.53209 3.239145e+00 0.0719418044
## 245  0.786922781 13.53669 3.514204e-01 0.5533295806
## 246 -1.312536147 13.46314 1.496909e+00 0.2409764066
## 247  0.000000000 13.50848 0.000000e+00 1.0000000000
## 248 -4.694050423 13.65312 9.661124e+00 0.0018897394
## 249 -2.390836958 13.41546 3.984018e+00 0.0459730926
## 250 -0.075580322 13.59538 1.440089e-03 0.9697298402
## 251 -4.765956462 13.76573 9.709212e+00 0.0018409917
## 252  0.000000000 13.42899 0.000000e+00 1.0000000000
## 253 -0.276144489 13.47794 4.923497e-02 0.8244064352
## 254 -1.305051126 13.48828 1.424433e+00 0.2409764063
## 255 -1.984427827 13.80922 2.011920e+00 0.1561129102
## 256  0.000000000 13.57768 0.000000e+00 1.0000000000
## 257 -0.422692699 13.55251 9.905883e-02 0.7529715254
## 258 -4.223297491 13.57169 8.281895e+00 0.0040165257
## 259 -0.473484722 13.54507 1.238154e-01 0.7249434317
## 260 -3.035703067 13.70467 4.737272e+00 0.0295496405
## 261 -1.837594949 13.59744 1.926518e+00 0.1651847330
## 262 -2.014964807 13.47262 2.457832e+00 0.1169859271
## 263  0.460811725 13.59989 1.339080e-01 0.7144251839
## 264 -1.516104120 13.64070 1.188209e+00 0.2757291011
## 265 -3.039659711 13.54518 4.678148e+00 0.0305829093
## 266 -1.241329636 13.69606 1.285848e+00 0.2568539763
## 267  0.003533849 13.54823 2.412880e-05 0.9960808628
## 268 -1.376290323 13.47267 1.523726e+00 0.2409764103
## 269  1.223200991 13.70797 9.383104e-01 0.3327466855
## 270 -0.357537840 13.68056 7.797053e-02 0.7800751321
## 271 -3.502898214 13.63113 5.944375e+00 0.0147893908
## 272  2.590724618 13.56320 3.659375e+00 0.0557958925
## 273 -1.887981057 13.60526 1.990724e+00 0.1583103287
## 274 -2.457088722 13.67028 3.333189e+00 0.0679383262
## 275 -2.347612656 13.59238 3.199180e+00 0.0737190462
## 276  2.779097255 13.63332 4.040564e+00 0.0444578126
## 277 -2.740978859 13.58571 4.064891e+00 0.0438221774
## 278 -1.304555327 13.90567 1.279137e+00 0.2580989043
## 279 -0.916768301 13.89772 4.590863e-01 0.4980740300
## 280  0.094271712 13.62857 4.565708e-03 0.9461298746
## 281 -4.639571577 14.01310 8.262842e+00 0.0040588446
## 282  0.000000000 13.83168 0.000000e+00 1.0000000000
## 283  0.000000000 13.72368 0.000000e+00 1.0000000000
## 284 -1.976682578 13.48675 2.580505e+00 0.1082329070
## 285 -2.750419725 13.46373 4.515558e+00 0.0336233648
## 286  0.616299070 13.69329 2.091276e-01 0.6474664067
## 287  0.592749133 13.61721 2.190795e-01 0.6397569896
## 288  0.311920067 13.87161 5.059953e-02 0.8220299732
## 289  0.000000000 13.54506 0.000000e+00 1.0000000000
## 290 -2.210165249 13.56988 2.540769e+00 0.1109865315
## 291  0.000000000 13.83223 0.000000e+00 1.0000000000
## 292 -1.804363568 13.79365 1.783188e+00 0.1818023570
## 293 -1.333622300 13.44890 1.554511e+00 0.2409764078
## 294 -1.304501383 13.94724 1.271604e+00 0.2595051148
## 295  0.000000000 13.67015 0.000000e+00 1.0000000000
## 296 -0.724548908 13.56577 3.003486e-01 0.5836816856
## 297 -4.608035796 13.65890 9.356749e+00 0.0022301791
## 298 -0.681558400 13.47514 2.871780e-01 0.5920518829
## 299 -2.552878710 13.54658 3.569865e+00 0.0588789905
## 300  1.741668781 13.78278 1.592331e+00 0.2070361013
## 301 -0.695592092 13.42834 3.016397e-01 0.5828740851
## 302 -1.304966821 13.63758 1.335594e+00 0.2478524384
## 303 -1.387176569 14.26021 1.074526e+00 0.2999617703
## 304 -0.586479630 13.58066 1.796657e-01 0.6716739074
## 305 -0.626542066 13.64217 2.416713e-01 0.6230172612
## 306  3.734730455 13.68553 6.663420e+00 0.0098616274
## 307  0.069433131 13.70197 3.142762e-03 0.9552953611
## 308  0.000000000 13.46189 0.000000e+00 1.0000000000
## 309  0.663155924 13.55002 2.746272e-01 0.6197798520
## 310  0.000000000 13.44628 0.000000e+00 1.0000000000
## 311  3.065080452 13.50119 4.974344e+00 0.0257579926
## 312  0.480424389 13.52902 1.453159e-01 0.7030642081
## 313 -2.803112461 13.73746 4.174622e+00 0.0410716226
## 314 -0.667610810 13.70128 2.632502e-01 0.6079124071
## 315 -0.464644212 13.50855 1.397537e-01 0.7085375063
## 316 -4.469577790 13.93824 8.083748e+00 0.0044795224
## 317  0.000000000 13.45221 0.000000e+00 1.0000000000
## 318  5.021508338 13.63325 1.083282e+01 0.0010021747
## 319 -1.863662709 13.68708 1.802819e+00 0.1794162881
## 320 -0.955670677 13.55119 5.175566e-01 0.4719101768
## 321  0.000000000 13.77319 0.000000e+00 1.0000000000
## 322  0.000000000 13.67604 0.000000e+00 1.0000000000
## 323 -2.000736594 13.79374 2.389586e+00 0.1221918056
## 324  0.545318919 13.71259 1.914092e-01 0.6617600301
## 325 -2.055121441 13.65726 2.294419e+00 0.1298856340
## 326 -2.859422368 13.52498 4.205249e+00 0.0403367412
## 327  0.037677404 13.71382 1.254456e-03 0.9717472193
## 328 -3.709296805 13.62702 6.513799e+00 0.0107254131
## 329 -0.941755363 13.95378 4.257272e-01 0.5141147601
## 330 -1.845016266 13.61737 1.914912e+00 0.1664634365
## 331  1.143076463 13.52942 7.594427e-01 0.3835333149
## 332 -0.519835893 13.65637 1.417424e-01 0.7065664804
## 333 -2.024507739 13.43938 2.650263e+00 0.1035783955
## 334 -1.095789252 13.92288 6.401832e-01 0.4236719993
## 335 -1.422906882 13.62742 1.185236e+00 0.2763305905
## 336  3.168957776 13.50479 5.216260e+00 0.0224068729
## 337  0.000000000 13.58268 0.000000e+00 1.0000000000
## 338  2.201367154 13.46859 2.945159e+00 0.0861801072
## 339  3.115430945 13.49123 5.183933e+00 0.0228271528
## 340 -1.688958883 13.62782 1.614700e+00 0.2038752502
## 341  2.662602217 13.57032 3.865034e+00 0.0493422408
## 342  0.421046262 13.53667 1.095536e-01 0.7406630218
## 343 -1.557380990 13.45432 1.415334e+00 0.2342139277
## 344 -1.042118980 13.55560 6.370821e-01 0.4247968539
## 345 -1.305039821 13.50254 1.392972e+00 0.2409764063
##            FDR Nhood SpatialFDR        contrast
## 1   0.78936835     1 0.78842340 Age1wk - Age4wk
## 2   0.40337566     2 0.40275765 Age1wk - Age4wk
## 3   0.88611903     3 0.87904536 Age1wk - Age4wk
## 4   0.22228906     4 0.22155574 Age1wk - Age4wk
## 5   0.15287968     5 0.16078832 Age1wk - Age4wk
## 6   0.36697427     6 0.35447289 Age1wk - Age4wk
## 7   0.59753131     7 0.60094608 Age1wk - Age4wk
## 8   0.41586830     8 0.42017105 Age1wk - Age4wk
## 9   1.00000000     9 1.00000000 Age1wk - Age4wk
## 10  0.08133870    10 0.08392133 Age1wk - Age4wk
## 11  1.00000000    11 1.00000000 Age1wk - Age4wk
## 12  0.53879301    12 0.53407006 Age1wk - Age4wk
## 13  0.50868900    13 0.50697928 Age1wk - Age4wk
## 14  0.84000627    14 0.83558690 Age1wk - Age4wk
## 15  0.55627546    15 0.55290700 Age1wk - Age4wk
## 16  1.00000000    16 1.00000000 Age1wk - Age4wk
## 17  1.00000000    17 0.99931583 Age1wk - Age4wk
## 18  0.50868900    18 0.50444565 Age1wk - Age4wk
## 19  0.41804487    19 0.42512725 Age1wk - Age4wk
## 20  0.22140172    20 0.22155574 Age1wk - Age4wk
## 21  0.11902829    21 0.12452590 Age1wk - Age4wk
## 22  0.50868900    22 0.50402522 Age1wk - Age4wk
## 23  0.68078907    23 0.68223035 Age1wk - Age4wk
## 24  0.13880866    24 0.14930921 Age1wk - Age4wk
## 25  0.22140172    25 0.22146845 Age1wk - Age4wk
## 26  0.15067339    26 0.15710319 Age1wk - Age4wk
## 27  0.49260314    27 0.50402522 Age1wk - Age4wk
## 28  0.77528100    28 0.77495059 Age1wk - Age4wk
## 29  0.88241673    29 0.87805860 Age1wk - Age4wk
## 30  1.00000000    30 1.00000000 Age1wk - Age4wk
## 31  0.43173282    31 0.43706579 Age1wk - Age4wk
## 32  0.86877790    32 0.86295455 Age1wk - Age4wk
## 33  0.75688322    33 0.76040441 Age1wk - Age4wk
## 34  0.51708569    34 0.51418571 Age1wk - Age4wk
## 35  0.87509112    35 0.87023973 Age1wk - Age4wk
## 36  0.36697427    36 0.35447289 Age1wk - Age4wk
## 37  0.35437388    37 0.34346983 Age1wk - Age4wk
## 38  0.82876521    38 0.82442584 Age1wk - Age4wk
## 39  0.40499207    39 0.40651074 Age1wk - Age4wk
## 40  0.88241673    40 0.87805860 Age1wk - Age4wk
## 41  0.50868900    41 0.50444565 Age1wk - Age4wk
## 42  0.89320361    42 0.88925334 Age1wk - Age4wk
## 43  0.50868900    43 0.50697928 Age1wk - Age4wk
## 44  1.00000000    44 1.00000000 Age1wk - Age4wk
## 45  0.08133870    45 0.08392133 Age1wk - Age4wk
## 46  0.17885309    46 0.17889753 Age1wk - Age4wk
## 47  1.00000000    47 1.00000000 Age1wk - Age4wk
## 48  0.50868900    48 0.50402522 Age1wk - Age4wk
## 49  0.50868900    49 0.50444565 Age1wk - Age4wk
## 50  1.00000000    50 1.00000000 Age1wk - Age4wk
## 51  0.14271443    51 0.14930921 Age1wk - Age4wk
## 52  0.40144101    52 0.40275765 Age1wk - Age4wk
## 53  0.68402621    53 0.68713994 Age1wk - Age4wk
## 54  0.91440707    54 0.91471617 Age1wk - Age4wk
## 55  1.00000000    55 1.00000000 Age1wk - Age4wk
## 56  0.50868900    56 0.50402522 Age1wk - Age4wk
## 57  0.88241673    57 0.87805860 Age1wk - Age4wk
## 58  0.47546413    58 0.48402019 Age1wk - Age4wk
## 59  0.89320361    59 0.88925334 Age1wk - Age4wk
## 60  1.00000000    60 1.00000000 Age1wk - Age4wk
## 61  1.00000000    61 1.00000000 Age1wk - Age4wk
## 62  0.39759682    62 0.39963970 Age1wk - Age4wk
## 63  0.88241673    63 0.87805860 Age1wk - Age4wk
## 64  0.36608189    64 0.35324242 Age1wk - Age4wk
## 65  0.08133870    65 0.08392133 Age1wk - Age4wk
## 66  1.00000000    66 1.00000000 Age1wk - Age4wk
## 67  0.93927185    67 0.92854620 Age1wk - Age4wk
## 68  0.12174161    68 0.13147874 Age1wk - Age4wk
## 69  0.17885309    69 0.17889753 Age1wk - Age4wk
## 70  0.77405085    70 0.77368660 Age1wk - Age4wk
## 71  0.50868900    71 0.50444565 Age1wk - Age4wk
## 72  0.22685997    72 0.22685819 Age1wk - Age4wk
## 73  0.08133870    73 0.07905304 Age1wk - Age4wk
## 74  0.78936835    74 0.78842340 Age1wk - Age4wk
## 75  1.00000000    75 1.00000000 Age1wk - Age4wk
## 76  0.10896454    76 0.11202792 Age1wk - Age4wk
## 77  1.00000000    77 1.00000000 Age1wk - Age4wk
## 78  0.38364913    78 0.37813244 Age1wk - Age4wk
## 79  0.28664336    79 0.28179301 Age1wk - Age4wk
## 80  0.24658642    80 0.24653670 Age1wk - Age4wk
## 81  0.38364913    81 0.37898401 Age1wk - Age4wk
## 82  0.50868900    82 0.50697928 Age1wk - Age4wk
## 83  0.97897741    83 0.96483454 Age1wk - Age4wk
## 84  0.08133870    84 0.08392133 Age1wk - Age4wk
## 85  1.00000000    85 1.00000000 Age1wk - Age4wk
## 86  0.36697427    86 0.35447289 Age1wk - Age4wk
## 87  1.00000000    87 1.00000000 Age1wk - Age4wk
## 88  1.00000000    88 1.00000000 Age1wk - Age4wk
## 89  1.00000000    89 1.00000000 Age1wk - Age4wk
## 90  0.22140172    90 0.22155574 Age1wk - Age4wk
## 91  0.57080772    91 0.57097900 Age1wk - Age4wk
## 92  0.90457443    92 0.89893083 Age1wk - Age4wk
## 93  0.39759682    93 0.39963970 Age1wk - Age4wk
## 94  1.00000000    94 0.98471886 Age1wk - Age4wk
## 95  0.50868900    95 0.50402522 Age1wk - Age4wk
## 96  0.14655859    96 0.15271260 Age1wk - Age4wk
## 97  0.28821180    97 0.28429955 Age1wk - Age4wk
## 98  1.00000000    98 1.00000000 Age1wk - Age4wk
## 99  0.07424195    99 0.06870498 Age1wk - Age4wk
## 100 0.60799002   100 0.61254059 Age1wk - Age4wk
## 101 0.38364913   101 0.37813244 Age1wk - Age4wk
## 102 0.12015121   102 0.12741079 Age1wk - Age4wk
## 103 0.50868900   103 0.50444565 Age1wk - Age4wk
## 104 0.45772838   104 0.46810870 Age1wk - Age4wk
## 105 1.00000000   105 1.00000000 Age1wk - Age4wk
## 106 1.00000000   106 1.00000000 Age1wk - Age4wk
## 107 0.40686679   107 0.41007591 Age1wk - Age4wk
## 108 1.00000000   108 1.00000000 Age1wk - Age4wk
## 109 0.32672678   109 0.31652868 Age1wk - Age4wk
## 110 0.82215891   110 0.81929420 Age1wk - Age4wk
## 111 0.36697427   111 0.35447289 Age1wk - Age4wk
## 112 0.45772838   112 0.46828929 Age1wk - Age4wk
## 113 0.10896454   113 0.11202792 Age1wk - Age4wk
## 114 1.00000000   114 1.00000000 Age1wk - Age4wk
## 115 1.00000000   115 1.00000000 Age1wk - Age4wk
## 116 0.49260314   116 0.50402522 Age1wk - Age4wk
## 117 1.00000000   117 1.00000000 Age1wk - Age4wk
## 118 0.46988040   118 0.48072713 Age1wk - Age4wk
## 119 0.11049181   119 0.11202792 Age1wk - Age4wk
## 120 1.00000000   120 1.00000000 Age1wk - Age4wk
## 121 0.28247570   121 0.27848344 Age1wk - Age4wk
## 122 0.14655859   122 0.15271260 Age1wk - Age4wk
## 123 0.39759682   123 0.39944487 Age1wk - Age4wk
## 124 0.50868900   124 0.50402522 Age1wk - Age4wk
## 125 0.88697410   125 0.88167879 Age1wk - Age4wk
## 126 0.47855135   126 0.48693653 Age1wk - Age4wk
## 127 0.50868900   127 0.50402522 Age1wk - Age4wk
## 128 0.27100713   128 0.26811722 Age1wk - Age4wk
## 129 0.10896454   129 0.11202792 Age1wk - Age4wk
## 130 0.15992503   130 0.16822190 Age1wk - Age4wk
## 131 1.00000000   131 1.00000000 Age1wk - Age4wk
## 132 1.00000000   132 0.99931583 Age1wk - Age4wk
## 133 0.48623993   133 0.49661215 Age1wk - Age4wk
## 134 1.00000000   134 1.00000000 Age1wk - Age4wk
## 135 0.97897741   135 0.96483454 Age1wk - Age4wk
## 136 0.71205691   136 0.71618951 Age1wk - Age4wk
## 137 1.00000000   137 1.00000000 Age1wk - Age4wk
## 138 1.00000000   138 1.00000000 Age1wk - Age4wk
## 139 1.00000000   139 1.00000000 Age1wk - Age4wk
## 140 0.62053583   140 0.62778821 Age1wk - Age4wk
## 141 0.08133870   141 0.07905304 Age1wk - Age4wk
## 142 0.51096852   142 0.50697928 Age1wk - Age4wk
## 143 0.22685997   143 0.22685819 Age1wk - Age4wk
## 144 0.35364868   144 0.34083824 Age1wk - Age4wk
## 145 1.00000000   145 1.00000000 Age1wk - Age4wk
## 146 1.00000000   146 1.00000000 Age1wk - Age4wk
## 147 0.38364913   147 0.37813244 Age1wk - Age4wk
## 148 0.11360353   148 0.11513626 Age1wk - Age4wk
## 149 0.90528029   149 0.90169697 Age1wk - Age4wk
## 150 0.12174161   150 0.13147874 Age1wk - Age4wk
## 151 0.98810771   151 0.97361450 Age1wk - Age4wk
## 152 0.36608189   152 0.35324242 Age1wk - Age4wk
## 153 0.11902829   153 0.12452590 Age1wk - Age4wk
## 154 0.59539854   154 0.59658531 Age1wk - Age4wk
## 155 0.08374855   155 0.08562298 Age1wk - Age4wk
## 156 0.88260405   156 0.87805860 Age1wk - Age4wk
## 157 0.11205963   157 0.11346595 Age1wk - Age4wk
## 158 0.14271443   158 0.14930921 Age1wk - Age4wk
## 159 0.67038909   159 0.67552707 Age1wk - Age4wk
## 160 0.29233415   160 0.28705279 Age1wk - Age4wk
## 161 1.00000000   161 1.00000000 Age1wk - Age4wk
## 162 0.27223633   162 0.27007189 Age1wk - Age4wk
## 163 1.00000000   163 1.00000000 Age1wk - Age4wk
## 164 0.93927185   164 0.92854620 Age1wk - Age4wk
## 165 1.00000000   165 1.00000000 Age1wk - Age4wk
## 166 0.50868900   166 0.50402522 Age1wk - Age4wk
## 167 0.71205691   167 0.71618951 Age1wk - Age4wk
## 168 1.00000000   168 1.00000000 Age1wk - Age4wk
## 169 0.82215891   169 0.81929420 Age1wk - Age4wk
## 170 1.00000000   170 1.00000000 Age1wk - Age4wk
## 171 0.89320361   171 0.88925334 Age1wk - Age4wk
## 172 0.38364913   172 0.37898401 Age1wk - Age4wk
## 173 0.36697427   173 0.35447289 Age1wk - Age4wk
## 174 0.14270688   174 0.14930921 Age1wk - Age4wk
## 175 1.00000000   175 1.00000000 Age1wk - Age4wk
## 176 0.07424195   176 0.06870498 Age1wk - Age4wk
## 177 0.38364913   177 0.37813244 Age1wk - Age4wk
## 178 0.10896454   178 0.11139561 Age1wk - Age4wk
## 179 1.00000000   179 1.00000000 Age1wk - Age4wk
## 180 0.07424195   180 0.06870498 Age1wk - Age4wk
## 181 1.00000000   181 1.00000000 Age1wk - Age4wk
## 182 0.07424195   182 0.06870498 Age1wk - Age4wk
## 183 0.50868900   183 0.50402522 Age1wk - Age4wk
## 184 0.68078907   184 0.68223035 Age1wk - Age4wk
## 185 0.90112727   185 0.89441961 Age1wk - Age4wk
## 186 1.00000000   186 1.00000000 Age1wk - Age4wk
## 187 0.62078476   187 0.62778821 Age1wk - Age4wk
## 188 0.17885309   188 0.17889753 Age1wk - Age4wk
## 189 0.66020583   189 0.66516095 Age1wk - Age4wk
## 190 0.93927185   190 0.92854620 Age1wk - Age4wk
## 191 0.28462063   191 0.28024533 Age1wk - Age4wk
## 192 0.50868900   192 0.50402522 Age1wk - Age4wk
## 193 0.65404846   193 0.65990441 Age1wk - Age4wk
## 194 0.35364868   194 0.34083824 Age1wk - Age4wk
## 195 0.50868900   195 0.50612601 Age1wk - Age4wk
## 196 0.74194766   196 0.74331353 Age1wk - Age4wk
## 197 0.38626589   197 0.38338474 Age1wk - Age4wk
## 198 0.17885309   198 0.17889753 Age1wk - Age4wk
## 199 0.93927185   199 0.92854620 Age1wk - Age4wk
## 200 0.97897741   200 0.96483454 Age1wk - Age4wk
## 201 0.88241673   201 0.87805860 Age1wk - Age4wk
## 202 0.15067339   202 0.15710319 Age1wk - Age4wk
## 203 0.62269710   203 0.62851494 Age1wk - Age4wk
## 204 0.50868900   204 0.50402522 Age1wk - Age4wk
## 205 0.31371427   205 0.30956159 Age1wk - Age4wk
## 206 0.11205963   206 0.11346595 Age1wk - Age4wk
## 207 0.51708569   207 0.51354944 Age1wk - Age4wk
## 208 1.00000000   208 1.00000000 Age1wk - Age4wk
## 209 0.50868900   209 0.50402522 Age1wk - Age4wk
## 210 0.30486431   210 0.30113602 Age1wk - Age4wk
## 211 1.00000000   211 1.00000000 Age1wk - Age4wk
## 212 0.22228906   212 0.22155574 Age1wk - Age4wk
## 213 1.00000000   213 0.98471886 Age1wk - Age4wk
## 214 1.00000000   214 1.00000000 Age1wk - Age4wk
## 215 0.12174161   215 0.13126650 Age1wk - Age4wk
## 216 0.35364868   216 0.34083824 Age1wk - Age4wk
## 217 0.95164745   217 0.93882627 Age1wk - Age4wk
## 218 0.87489909   218 0.87023973 Age1wk - Age4wk
## 219 1.00000000   219 1.00000000 Age1wk - Age4wk
## 220 0.50868900   220 0.50402522 Age1wk - Age4wk
## 221 1.00000000   221 1.00000000 Age1wk - Age4wk
## 222 1.00000000   222 1.00000000 Age1wk - Age4wk
## 223 0.35364868   223 0.34083824 Age1wk - Age4wk
## 224 0.90609662   224 0.90626431 Age1wk - Age4wk
## 225 1.00000000   225 1.00000000 Age1wk - Age4wk
## 226 0.22228906   226 0.22155574 Age1wk - Age4wk
## 227 0.90110269   227 0.89441961 Age1wk - Age4wk
## 228 0.36697427   228 0.35447289 Age1wk - Age4wk
## 229 0.14271443   229 0.14930921 Age1wk - Age4wk
## 230 1.00000000   230 1.00000000 Age1wk - Age4wk
## 231 1.00000000   231 1.00000000 Age1wk - Age4wk
## 232 0.69014985   232 0.69528083 Age1wk - Age4wk
## 233 0.07424195   233 0.06870498 Age1wk - Age4wk
## 234 0.28247570   234 0.27930144 Age1wk - Age4wk
## 235 0.60829219   235 0.61452470 Age1wk - Age4wk
## 236 0.36608189   236 0.35324242 Age1wk - Age4wk
## 237 0.89466129   237 0.88925334 Age1wk - Age4wk
## 238 0.14271443   238 0.14930921 Age1wk - Age4wk
## 239 1.00000000   239 1.00000000 Age1wk - Age4wk
## 240 1.00000000   240 1.00000000 Age1wk - Age4wk
## 241 1.00000000   241 1.00000000 Age1wk - Age4wk
## 242 0.36608189   242 0.35324242 Age1wk - Age4wk
## 243 0.07424195   243 0.06870498 Age1wk - Age4wk
## 244 0.29199909   244 0.28705279 Age1wk - Age4wk
## 245 0.86877790   245 0.86295455 Age1wk - Age4wk
## 246 0.50868900   246 0.50402522 Age1wk - Age4wk
## 247 1.00000000   247 1.00000000 Age1wk - Age4wk
## 248 0.07424195   248 0.06870498 Age1wk - Age4wk
## 249 0.22658167   249 0.22537347 Age1wk - Age4wk
## 250 1.00000000   250 1.00000000 Age1wk - Age4wk
## 251 0.07424195   251 0.06870498 Age1wk - Age4wk
## 252 1.00000000   252 1.00000000 Age1wk - Age4wk
## 253 1.00000000   253 1.00000000 Age1wk - Age4wk
## 254 0.50868900   254 0.50402522 Age1wk - Age4wk
## 255 0.41804487   255 0.42512725 Age1wk - Age4wk
## 256 1.00000000   256 1.00000000 Age1wk - Age4wk
## 257 0.98028368   257 0.96500713 Age1wk - Age4wk
## 258 0.08133870   258 0.08392133 Age1wk - Age4wk
## 259 0.96194417   259 0.95048927 Age1wk - Age4wk
## 260 0.17885309   260 0.17889753 Age1wk - Age4wk
## 261 0.43173282   261 0.43706579 Age1wk - Age4wk
## 262 0.36697427   262 0.35447289 Age1wk - Age4wk
## 263 0.95164745   263 0.94002750 Age1wk - Age4wk
## 264 0.52670748   264 0.52299681 Age1wk - Age4wk
## 265 0.18191558   265 0.18085154 Age1wk - Age4wk
## 266 0.50868900   266 0.50697928 Age1wk - Age4wk
## 267 1.00000000   267 1.00000000 Age1wk - Age4wk
## 268 0.50868900   268 0.50402522 Age1wk - Age4wk
## 269 0.60799002   269 0.61254059 Age1wk - Age4wk
## 270 1.00000000   270 0.98471886 Age1wk - Age4wk
## 271 0.13790108   271 0.14930921 Age1wk - Age4wk
## 272 0.25666111   272 0.25663070 Age1wk - Age4wk
## 273 0.42013126   273 0.42590436 Age1wk - Age4wk
## 274 0.28583808   274 0.28179301 Age1wk - Age4wk
## 275 0.29233415   275 0.28705279 Age1wk - Age4wk
## 276 0.22228906   276 0.22155574 Age1wk - Age4wk
## 277 0.22228906   277 0.22155574 Age1wk - Age4wk
## 278 0.50868900   278 0.50697928 Age1wk - Age4wk
## 279 0.80673963   279 0.80811918 Age1wk - Age4wk
## 280 1.00000000   280 1.00000000 Age1wk - Age4wk
## 281 0.08133870   281 0.08392133 Age1wk - Age4wk
## 282 1.00000000   282 1.00000000 Age1wk - Age4wk
## 283 1.00000000   283 1.00000000 Age1wk - Age4wk
## 284 0.36608189   284 0.35324242 Age1wk - Age4wk
## 285 0.19661120   285 0.19302778 Age1wk - Age4wk
## 286 0.90609662   286 0.90613228 Age1wk - Age4wk
## 287 0.90457443   287 0.89893083 Age1wk - Age4wk
## 288 1.00000000   288 1.00000000 Age1wk - Age4wk
## 289 1.00000000   289 1.00000000 Age1wk - Age4wk
## 290 0.36697427   290 0.35447289 Age1wk - Age4wk
## 291 1.00000000   291 1.00000000 Age1wk - Age4wk
## 292 0.45782345   292 0.46923166 Age1wk - Age4wk
## 293 0.50868900   293 0.50402522 Age1wk - Age4wk
## 294 0.50868900   294 0.50697928 Age1wk - Age4wk
## 295 1.00000000   295 1.00000000 Age1wk - Age4wk
## 296 0.88241673   296 0.87805860 Age1wk - Age4wk
## 297 0.07694118   297 0.07219674 Age1wk - Age4wk
## 298 0.88423333   298 0.87805860 Age1wk - Age4wk
## 299 0.26727963   299 0.26358473 Age1wk - Age4wk
## 300 0.49260314   300 0.50402522 Age1wk - Age4wk
## 301 0.88241673   301 0.87805860 Age1wk - Age4wk
## 302 0.50868900   302 0.50444565 Age1wk - Age4wk
## 303 0.56242832   303 0.56118631 Age1wk - Age4wk
## 304 0.92690999   304 0.92854620 Age1wk - Age4wk
## 305 0.89558731   305 0.89138603 Age1wk - Age4wk
## 306 0.11731936   306 0.11991309 Age1wk - Age4wk
## 307 1.00000000   307 1.00000000 Age1wk - Age4wk
## 308 1.00000000   308 1.00000000 Age1wk - Age4wk
## 309 0.89466129   309 0.88925334 Age1wk - Age4wk
## 310 1.00000000   310 1.00000000 Age1wk - Age4wk
## 311 0.17089437   311 0.17889753 Age1wk - Age4wk
## 312 0.95114957   312 0.93882627 Age1wk - Age4wk
## 313 0.22140172   313 0.22155574 Age1wk - Age4wk
## 314 0.89320361   314 0.88925334 Age1wk - Age4wk
## 315 0.95114957   315 0.93882627 Age1wk - Age4wk
## 316 0.08133870   316 0.08392133 Age1wk - Age4wk
## 317 1.00000000   317 1.00000000 Age1wk - Age4wk
## 318 0.07424195   318 0.06870498 Age1wk - Age4wk
## 319 0.45772838   319 0.46810870 Age1wk - Age4wk
## 320 0.77528100   320 0.77495059 Age1wk - Age4wk
## 321 1.00000000   321 1.00000000 Age1wk - Age4wk
## 322 1.00000000   322 1.00000000 Age1wk - Age4wk
## 323 0.37978534   323 0.36881269 Age1wk - Age4wk
## 324 0.91689643   324 0.91844991 Age1wk - Age4wk
## 325 0.38364913   325 0.37813244 Age1wk - Age4wk
## 326 0.22140172   326 0.22155574 Age1wk - Age4wk
## 327 1.00000000   327 1.00000000 Age1wk - Age4wk
## 328 0.11902829   328 0.12452590 Age1wk - Age4wk
## 329 0.82215891   329 0.81929420 Age1wk - Age4wk
## 330 0.43180365   330 0.43777937 Age1wk - Age4wk
## 331 0.67167002   331 0.67595323 Age1wk - Age4wk
## 332 0.95114957   332 0.93882627 Age1wk - Age4wk
## 333 0.36608189   333 0.35318631 Age1wk - Age4wk
## 334 0.71490202   334 0.71651981 Age1wk - Age4wk
## 335 0.52670748   335 0.52299681 Age1wk - Age4wk
## 336 0.15750735   336 0.16607809 Age1wk - Age4wk
## 337 1.00000000   337 1.00000000 Age1wk - Age4wk
## 338 0.32672678   338 0.31652868 Age1wk - Age4wk
## 339 0.15750735   339 0.16607809 Age1wk - Age4wk
## 340 0.49260314   340 0.50402522 Age1wk - Age4wk
## 341 0.23319278   341 0.23400689 Age1wk - Age4wk
## 342 0.97897741   342 0.96483454 Age1wk - Age4wk
## 343 0.50868900   343 0.50402522 Age1wk - Age4wk
## 344 0.71490202   344 0.71651981 Age1wk - Age4wk
## 345 0.50868900   345 0.50402522 Age1wk - Age4wk
##     PValue_adj_withinNhood
## 1             0.4850611329
## 2             0.1449813962
## 3             0.5958829418
## 4             0.0429890352
## 5             0.0212702168
## 6             0.1139488410
## 7             0.3238792907
## 8             0.1530877495
## 9             0.9841738976
## 10            0.0044186929
## 11            0.9069024878
## 12            0.2842328324
## 13            0.2572220424
## 14            0.5307865730
## 15            0.2950678547
## 16            1.0000000000
## 17            0.7995833597
## 18            0.2467555115
## 19            0.1563124305
## 20            0.0400970510
## 21            0.0110403050
## 22            0.2409764063
## 23            0.3922087813
## 24            0.0152890694
## 25            0.0389286509
## 26            0.0205265195
## 27            0.2057745727
## 28            0.4700030900
## 29            0.5848030831
## 30            0.9565854380
## 31            0.1651790616
## 32            0.5540032980
## 33            0.4541299330
## 34            0.2682850402
## 35            0.5631021139
## 36            0.1170062904
## 37            0.0986083837
## 38            0.5212813073
## 39            0.1467362590
## 40            0.5751149500
## 41            0.2494321188
## 42            0.6088552483
## 43            0.2591459898
## 44            0.8498421703
## 45            0.0035709546
## 46            0.0293144552
## 47            1.0000000000
## 48            0.2409764078
## 49            0.2508526933
## 50            0.8715943487
## 51            0.0176221369
## 52            0.1431224460
## 53            0.3965369305
## 54            0.6573129098
## 55            0.9867570025
## 56            0.2409764103
## 57            0.5774588540
## 58            0.1915638082
## 59            0.6128687161
## 60            0.9400380380
## 61            0.9829060358
## 62            0.1405994542
## 63            0.5857200898
## 64            0.1065145814
## 65            0.0043300806
## 66            1.0000000000
## 67            0.6915218824
## 68            0.0127034726
## 69            0.0285061004
## 70            0.4666741338
## 71            0.2493440054
## 72            0.0473446891
## 73            0.0028528939
## 74            0.4839915537
## 75            1.0000000000
## 76            0.0075223258
## 77            1.0000000000
## 78            0.1294035773
## 79            0.0689605771
## 80            0.0528909996
## 81            0.1311665641
## 82            0.2571302364
## 83            0.7491305370
## 84            0.0042708590
## 85            1.0000000000
## 86            0.1158842143
## 87            1.0000000000
## 88            0.9788789831
## 89            1.0000000000
## 90            0.0410237980
## 91            0.3060852990
## 92            0.6391942133
## 93            0.1403931487
## 94            0.7825580168
## 95            0.2413169209
## 96            0.0191163382
## 97            0.0701733070
## 98            0.8748280008
## 99            0.0016080060
## 100           0.3330727919
## 101           0.1273686104
## 102           0.0114927245
## 103           0.2492049891
## 104           0.1792019824
## 105           1.0000000000
## 106           1.0000000000
## 107           0.1485948292
## 108           0.9403737342
## 109           0.0856876040
## 110           0.5124180903
## 111           0.1166180759
## 112           0.1804378554
## 113           0.0075801416
## 114           0.8587468293
## 115           0.9321837993
## 116           0.2052935815
## 117           0.8130559691
## 118           0.1879521610
## 119           0.0080066531
## 120           1.0000000000
## 121           0.0647004127
## 122           0.0187720218
## 123           0.1393081611
## 124           0.2246742265
## 125           0.5990288826
## 126           0.1941947508
## 127           0.2244517583
## 128           0.0604856499
## 129           0.0071856010
## 130           0.0236410907
## 131           1.0000000000
## 132           0.8000192392
## 133           0.1987241465
## 134           1.0000000000
## 135           0.7489977090
## 136           0.4189784128
## 137           1.0000000000
## 138           1.0000000000
## 139           0.9720149076
## 140           0.3435430274
## 141           0.0029779565
## 142           0.2621490683
## 143           0.0473210512
## 144           0.0967870326
## 145           1.0000000000
## 146           0.8100682659
## 147           0.1296992633
## 148           0.0092199968
## 149           0.6428802028
## 150           0.0123617711
## 151           0.7618453635
## 152           0.1059736593
## 153           0.0109202758
## 154           0.3209974721
## 155           0.0048549883
## 156           0.5884026980
## 157           0.0084607404
## 158           0.0174435850
## 159           0.3808587272
## 160           0.0733525423
## 161           1.0000000000
## 162           0.0615490827
## 163           0.9484345694
## 164           0.6839111355
## 165           1.0000000000
## 166           0.2159050463
## 167           0.4187230121
## 168           0.9607378208
## 169           0.5147429673
## 170           1.0000000000
## 171           0.6135920462
## 172           0.1312191234
## 173           0.1139087425
## 174           0.0161320823
## 175           1.0000000000
## 176           0.0008703279
## 177           0.1298392078
## 178           0.0066483491
## 179           1.0000000000
## 180           0.0014307364
## 181           1.0000000000
## 182           0.0012305354
## 183           0.2409764103
## 184           0.3926870259
## 185           0.6320950688
## 186           1.0000000000
## 187           0.3454802153
## 188           0.0294532578
## 189           0.3731598196
## 190           0.6911066527
## 191           0.0668239729
## 192           0.2423250385
## 193           0.3677837735
## 194           0.0972697908
## 195           0.2523882369
## 196           0.4430180246
## 197           0.1332337422
## 198           0.0283475510
## 199           0.6882916365
## 200           0.7446707638
## 201           0.5760377163
## 202           0.0204163551
## 203           0.3483493933
## 204           0.2288735246
## 205           0.0809291884
## 206           0.0087698840
## 207           0.2671604337
## 208           0.9427998597
## 209           0.2406286738
## 210           0.0777624918
## 211           0.9765753039
## 212           0.0441341204
## 213           0.7773748831
## 214           1.0000000000
## 215           0.0120486934
## 216           0.0961669865
## 217           0.7117482350
## 218           0.5604426076
## 219           1.0000000000
## 220           0.2409764063
## 221           1.0000000000
## 222           1.0000000000
## 223           0.0973815214
## 224           0.6487126537
## 225           1.0000000000
## 226           0.0440695793
## 227           0.6294659395
## 228           0.1104987700
## 229           0.0165797539
## 230           1.0000000000
## 231           1.0000000000
## 232           0.4020873010
## 233           0.0019367466
## 234           0.0655016108
## 235           0.3350014933
## 236           0.1063357997
## 237           0.6191477633
## 238           0.0177875957
## 239           1.0000000000
## 240           1.0000000000
## 241           1.0000000000
## 242           0.1079024396
## 243           0.0011624817
## 244           0.0719418044
## 245           0.5533295806
## 246           0.2409764066
## 247           1.0000000000
## 248           0.0018897394
## 249           0.0459730926
## 250           0.9697298402
## 251           0.0018409917
## 252           1.0000000000
## 253           0.8244064352
## 254           0.2409764063
## 255           0.1561129102
## 256           1.0000000000
## 257           0.7529715254
## 258           0.0040165257
## 259           0.7249434317
## 260           0.0295496405
## 261           0.1651847330
## 262           0.1169859271
## 263           0.7144251839
## 264           0.2757291011
## 265           0.0305829093
## 266           0.2568539763
## 267           0.9960808628
## 268           0.2409764103
## 269           0.3327466855
## 270           0.7800751321
## 271           0.0147893908
## 272           0.0557958925
## 273           0.1583103287
## 274           0.0679383262
## 275           0.0737190462
## 276           0.0444578126
## 277           0.0438221774
## 278           0.2580989043
## 279           0.4980740300
## 280           0.9461298746
## 281           0.0040588446
## 282           1.0000000000
## 283           1.0000000000
## 284           0.1082329070
## 285           0.0336233648
## 286           0.6474664067
## 287           0.6397569896
## 288           0.8220299732
## 289           1.0000000000
## 290           0.1109865315
## 291           1.0000000000
## 292           0.1818023570
## 293           0.2409764078
## 294           0.2595051148
## 295           1.0000000000
## 296           0.5836816856
## 297           0.0022301791
## 298           0.5920518829
## 299           0.0588789905
## 300           0.2070361013
## 301           0.5828740851
## 302           0.2478524384
## 303           0.2999617703
## 304           0.6716739074
## 305           0.6230172612
## 306           0.0098616274
## 307           0.9552953611
## 308           1.0000000000
## 309           0.6197798520
## 310           1.0000000000
## 311           0.0257579926
## 312           0.7030642081
## 313           0.0410716226
## 314           0.6079124071
## 315           0.7085375063
## 316           0.0044795224
## 317           1.0000000000
## 318           0.0010021747
## 319           0.1794162881
## 320           0.4719101768
## 321           1.0000000000
## 322           1.0000000000
## 323           0.1221918056
## 324           0.6617600301
## 325           0.1298856340
## 326           0.0403367412
## 327           0.9717472193
## 328           0.0107254131
## 329           0.5141147601
## 330           0.1664634365
## 331           0.3835333149
## 332           0.7065664804
## 333           0.1035783955
## 334           0.4236719993
## 335           0.2763305905
## 336           0.0224068729
## 337           1.0000000000
## 338           0.0861801072
## 339           0.0228271528
## 340           0.2038752502
## 341           0.0493422408
## 342           0.7406630218
## 343           0.2342139277
## 344           0.4247968539
## 345           0.2409764063
## 
## $artifacts$design_df
##        Sample  Age
## 1_1wk   1_1wk  1wk
## 1_4wk   1_4wk  4wk
## 1_16wk 1_16wk 16wk
## 1_32wk 1_32wk 32wk
## 1_52wk 1_52wk 52wk
## 2_32wk 2_32wk 32wk
## 2_4wk   2_4wk  4wk
## 2_1wk   2_1wk  1wk
## 2_16wk 2_16wk 16wk
## 2_52wk 2_52wk 52wk
## 3_4wk   3_4wk  4wk
## 3_1wk   3_1wk  1wk
## 3_52wk 3_52wk 52wk
## 3_16wk 3_16wk 16wk
## 3_32wk 3_32wk 32wk
## 4_1wk   4_1wk  1wk
## 4_16wk 4_16wk 16wk
## 4_4wk   4_4wk  4wk
## 4_32wk 4_32wk 32wk
## 4_52wk 4_52wk 52wk
## 5_32wk 5_32wk 32wk
## 5_52wk 5_52wk 52wk
## 5_1wk   5_1wk  1wk
## 5_4wk   5_4wk  4wk
## 5_16wk 5_16wk 16wk
## 
## $artifacts$formula
## [1] "~0 + Age"
## 
## $artifacts$contrasts
## [1] "Age1wk - Age4wk"
## 
## 
## $params
## $params$k1
## [1] 11
## 
## $params$k2
## [1] 11
## 
## $params$d1
## [1] 40
## 
## $params$d2
## [1] 40
## 
## $params$d3
## [1] 30
## 
## $params$prop
## [1] 0.2
## 
## $params$overlap
## [1] 1
## 
## $params$per_contrast
## [1] TRUE
## 
## $params$is_refined
## [1] TRUE
## 
## $params$refinement_scheme
## [1] "graph"
## 
## $params$adjustment
## [1] "BH"
## 
## $params$glmm
## [1] FALSE
## 
## $params$random_effect
## NULL
## 
## $params$glmm_solver
## [1] "Fisher"
## 
## $params$REML
## [1] TRUE
## 
## $params$max.iters
## [1] 50
## 
## $params$fail.on.error
## [1] FALSE
## 
## $params$seed
## [1] 2025
## 
## 
## $summary
## $summary$n_nhood_results
## [1] 345
## 
## $summary$n_samples
## [1] 25
## 
## 
## $created_at
## [1] "2026-10-23 21:04:46 CST"
## 
## $da_results
##            logFC   logCPM            F       PValue
## 1    0.885424822 13.75617 4.875157e-01 0.4850611329
## 2   -2.018265469 13.53681 2.124756e+00 0.1449813962
## 3   -0.680401872 13.51842 2.812763e-01 0.5958829418
## 4   -2.794520000 13.62681 4.097346e+00 0.0429890352
## 5   -3.277441011 13.71092 5.306940e+00 0.0212702168
## 6   -2.214307812 13.67219 2.499216e+00 0.1139488410
## 7    1.412216917 14.07307 9.733557e-01 0.3238792907
## 8   -1.919662609 13.76313 2.041661e+00 0.1530877495
## 9    0.303862651 13.48961 5.601722e-02 0.9841738976
## 10  -4.163369017 13.53267 8.108558e+00 0.0044186929
## 11   0.149068083 13.87199 1.367748e-02 0.9069024878
## 12  -1.417661379 13.59763 1.146917e+00 0.2842328324
## 13  -1.241263608 13.66324 1.283859e+00 0.2572220424
## 14  -0.800870659 13.54175 3.929251e-01 0.5307865730
## 15  -1.477094427 14.02593 1.096520e+00 0.2950678547
## 16   0.000000000 13.89199 0.000000e+00 1.0000000000
## 17  -0.341245797 13.94449 6.446325e-02 0.7995833597
## 18  -1.304968439 13.60053 1.341808e+00 0.2467555115
## 19   1.854603060 13.64907 2.009981e+00 0.1563124305
## 20   2.855523682 13.79009 4.215366e+00 0.0400970510
## 21   3.667647023 13.64408 6.462310e+00 0.0110403050
## 22  -1.305051937 13.48726 1.427080e+00 0.2409764063
## 23  -1.175998323 13.51276 7.321751e-01 0.3922087813
## 24   3.422555109 13.55506 5.885783e+00 0.0152890694
## 25  -3.004123564 13.79703 4.265605e+00 0.0389286509
## 26  -3.238732140 13.56568 5.369028e+00 0.0205265195
## 27  -1.762332117 13.67659 1.601210e+00 0.2057745727
## 28  -0.914347458 13.71745 5.220263e-01 0.4700030900
## 29  -0.700049973 13.60289 2.985619e-01 0.5848030831
## 30  -0.102780014 13.46814 2.963816e-03 0.9565854380
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## 317  0.000000000 13.45221 0.000000e+00 1.0000000000
## 318  5.021508338 13.63325 1.083282e+01 0.0010021747
## 319 -1.863662709 13.68708 1.802819e+00 0.1794162881
## 320 -0.955670677 13.55119 5.175566e-01 0.4719101768
## 321  0.000000000 13.77319 0.000000e+00 1.0000000000
## 322  0.000000000 13.67604 0.000000e+00 1.0000000000
## 323 -2.000736594 13.79374 2.389586e+00 0.1221918056
## 324  0.545318919 13.71259 1.914092e-01 0.6617600301
## 325 -2.055121441 13.65726 2.294419e+00 0.1298856340
## 326 -2.859422368 13.52498 4.205249e+00 0.0403367412
## 327  0.037677404 13.71382 1.254456e-03 0.9717472193
## 328 -3.709296805 13.62702 6.513799e+00 0.0107254131
## 329 -0.941755363 13.95378 4.257272e-01 0.5141147601
## 330 -1.845016266 13.61737 1.914912e+00 0.1664634365
## 331  1.143076463 13.52942 7.594427e-01 0.3835333149
## 332 -0.519835893 13.65637 1.417424e-01 0.7065664804
## 333 -2.024507739 13.43938 2.650263e+00 0.1035783955
## 334 -1.095789252 13.92288 6.401832e-01 0.4236719993
## 335 -1.422906882 13.62742 1.185236e+00 0.2763305905
## 336  3.168957776 13.50479 5.216260e+00 0.0224068729
## 337  0.000000000 13.58268 0.000000e+00 1.0000000000
## 338  2.201367154 13.46859 2.945159e+00 0.0861801072
## 339  3.115430945 13.49123 5.183933e+00 0.0228271528
## 340 -1.688958883 13.62782 1.614700e+00 0.2038752502
## 341  2.662602217 13.57032 3.865034e+00 0.0493422408
## 342  0.421046262 13.53667 1.095536e-01 0.7406630218
## 343 -1.557380990 13.45432 1.415334e+00 0.2342139277
## 344 -1.042118980 13.55560 6.370821e-01 0.4247968539
## 345 -1.305039821 13.50254 1.392972e+00 0.2409764063
##            FDR Nhood SpatialFDR        contrast
## 1   0.78936835     1 0.78842340 Age1wk - Age4wk
## 2   0.40337566     2 0.40275765 Age1wk - Age4wk
## 3   0.88611903     3 0.87904536 Age1wk - Age4wk
## 4   0.22228906     4 0.22155574 Age1wk - Age4wk
## 5   0.15287968     5 0.16078832 Age1wk - Age4wk
## 6   0.36697427     6 0.35447289 Age1wk - Age4wk
## 7   0.59753131     7 0.60094608 Age1wk - Age4wk
## 8   0.41586830     8 0.42017105 Age1wk - Age4wk
## 9   1.00000000     9 1.00000000 Age1wk - Age4wk
## 10  0.08133870    10 0.08392133 Age1wk - Age4wk
## 11  1.00000000    11 1.00000000 Age1wk - Age4wk
## 12  0.53879301    12 0.53407006 Age1wk - Age4wk
## 13  0.50868900    13 0.50697928 Age1wk - Age4wk
## 14  0.84000627    14 0.83558690 Age1wk - Age4wk
## 15  0.55627546    15 0.55290700 Age1wk - Age4wk
## 16  1.00000000    16 1.00000000 Age1wk - Age4wk
## 17  1.00000000    17 0.99931583 Age1wk - Age4wk
## 18  0.50868900    18 0.50444565 Age1wk - Age4wk
## 19  0.41804487    19 0.42512725 Age1wk - Age4wk
## 20  0.22140172    20 0.22155574 Age1wk - Age4wk
## 21  0.11902829    21 0.12452590 Age1wk - Age4wk
## 22  0.50868900    22 0.50402522 Age1wk - Age4wk
## 23  0.68078907    23 0.68223035 Age1wk - Age4wk
## 24  0.13880866    24 0.14930921 Age1wk - Age4wk
## 25  0.22140172    25 0.22146845 Age1wk - Age4wk
## 26  0.15067339    26 0.15710319 Age1wk - Age4wk
## 27  0.49260314    27 0.50402522 Age1wk - Age4wk
## 28  0.77528100    28 0.77495059 Age1wk - Age4wk
## 29  0.88241673    29 0.87805860 Age1wk - Age4wk
## 30  1.00000000    30 1.00000000 Age1wk - Age4wk
## 31  0.43173282    31 0.43706579 Age1wk - Age4wk
## 32  0.86877790    32 0.86295455 Age1wk - Age4wk
## 33  0.75688322    33 0.76040441 Age1wk - Age4wk
## 34  0.51708569    34 0.51418571 Age1wk - Age4wk
## 35  0.87509112    35 0.87023973 Age1wk - Age4wk
## 36  0.36697427    36 0.35447289 Age1wk - Age4wk
## 37  0.35437388    37 0.34346983 Age1wk - Age4wk
## 38  0.82876521    38 0.82442584 Age1wk - Age4wk
## 39  0.40499207    39 0.40651074 Age1wk - Age4wk
## 40  0.88241673    40 0.87805860 Age1wk - Age4wk
## 41  0.50868900    41 0.50444565 Age1wk - Age4wk
## 42  0.89320361    42 0.88925334 Age1wk - Age4wk
## 43  0.50868900    43 0.50697928 Age1wk - Age4wk
## 44  1.00000000    44 1.00000000 Age1wk - Age4wk
## 45  0.08133870    45 0.08392133 Age1wk - Age4wk
## 46  0.17885309    46 0.17889753 Age1wk - Age4wk
## 47  1.00000000    47 1.00000000 Age1wk - Age4wk
## 48  0.50868900    48 0.50402522 Age1wk - Age4wk
## 49  0.50868900    49 0.50444565 Age1wk - Age4wk
## 50  1.00000000    50 1.00000000 Age1wk - Age4wk
## 51  0.14271443    51 0.14930921 Age1wk - Age4wk
## 52  0.40144101    52 0.40275765 Age1wk - Age4wk
## 53  0.68402621    53 0.68713994 Age1wk - Age4wk
## 54  0.91440707    54 0.91471617 Age1wk - Age4wk
## 55  1.00000000    55 1.00000000 Age1wk - Age4wk
## 56  0.50868900    56 0.50402522 Age1wk - Age4wk
## 57  0.88241673    57 0.87805860 Age1wk - Age4wk
## 58  0.47546413    58 0.48402019 Age1wk - Age4wk
## 59  0.89320361    59 0.88925334 Age1wk - Age4wk
## 60  1.00000000    60 1.00000000 Age1wk - Age4wk
## 61  1.00000000    61 1.00000000 Age1wk - Age4wk
## 62  0.39759682    62 0.39963970 Age1wk - Age4wk
## 63  0.88241673    63 0.87805860 Age1wk - Age4wk
## 64  0.36608189    64 0.35324242 Age1wk - Age4wk
## 65  0.08133870    65 0.08392133 Age1wk - Age4wk
## 66  1.00000000    66 1.00000000 Age1wk - Age4wk
## 67  0.93927185    67 0.92854620 Age1wk - Age4wk
## 68  0.12174161    68 0.13147874 Age1wk - Age4wk
## 69  0.17885309    69 0.17889753 Age1wk - Age4wk
## 70  0.77405085    70 0.77368660 Age1wk - Age4wk
## 71  0.50868900    71 0.50444565 Age1wk - Age4wk
## 72  0.22685997    72 0.22685819 Age1wk - Age4wk
## 73  0.08133870    73 0.07905304 Age1wk - Age4wk
## 74  0.78936835    74 0.78842340 Age1wk - Age4wk
## 75  1.00000000    75 1.00000000 Age1wk - Age4wk
## 76  0.10896454    76 0.11202792 Age1wk - Age4wk
## 77  1.00000000    77 1.00000000 Age1wk - Age4wk
## 78  0.38364913    78 0.37813244 Age1wk - Age4wk
## 79  0.28664336    79 0.28179301 Age1wk - Age4wk
## 80  0.24658642    80 0.24653670 Age1wk - Age4wk
## 81  0.38364913    81 0.37898401 Age1wk - Age4wk
## 82  0.50868900    82 0.50697928 Age1wk - Age4wk
## 83  0.97897741    83 0.96483454 Age1wk - Age4wk
## 84  0.08133870    84 0.08392133 Age1wk - Age4wk
## 85  1.00000000    85 1.00000000 Age1wk - Age4wk
## 86  0.36697427    86 0.35447289 Age1wk - Age4wk
## 87  1.00000000    87 1.00000000 Age1wk - Age4wk
## 88  1.00000000    88 1.00000000 Age1wk - Age4wk
## 89  1.00000000    89 1.00000000 Age1wk - Age4wk
## 90  0.22140172    90 0.22155574 Age1wk - Age4wk
## 91  0.57080772    91 0.57097900 Age1wk - Age4wk
## 92  0.90457443    92 0.89893083 Age1wk - Age4wk
## 93  0.39759682    93 0.39963970 Age1wk - Age4wk
## 94  1.00000000    94 0.98471886 Age1wk - Age4wk
## 95  0.50868900    95 0.50402522 Age1wk - Age4wk
## 96  0.14655859    96 0.15271260 Age1wk - Age4wk
## 97  0.28821180    97 0.28429955 Age1wk - Age4wk
## 98  1.00000000    98 1.00000000 Age1wk - Age4wk
## 99  0.07424195    99 0.06870498 Age1wk - Age4wk
## 100 0.60799002   100 0.61254059 Age1wk - Age4wk
## 101 0.38364913   101 0.37813244 Age1wk - Age4wk
## 102 0.12015121   102 0.12741079 Age1wk - Age4wk
## 103 0.50868900   103 0.50444565 Age1wk - Age4wk
## 104 0.45772838   104 0.46810870 Age1wk - Age4wk
## 105 1.00000000   105 1.00000000 Age1wk - Age4wk
## 106 1.00000000   106 1.00000000 Age1wk - Age4wk
## 107 0.40686679   107 0.41007591 Age1wk - Age4wk
## 108 1.00000000   108 1.00000000 Age1wk - Age4wk
## 109 0.32672678   109 0.31652868 Age1wk - Age4wk
## 110 0.82215891   110 0.81929420 Age1wk - Age4wk
## 111 0.36697427   111 0.35447289 Age1wk - Age4wk
## 112 0.45772838   112 0.46828929 Age1wk - Age4wk
## 113 0.10896454   113 0.11202792 Age1wk - Age4wk
## 114 1.00000000   114 1.00000000 Age1wk - Age4wk
## 115 1.00000000   115 1.00000000 Age1wk - Age4wk
## 116 0.49260314   116 0.50402522 Age1wk - Age4wk
## 117 1.00000000   117 1.00000000 Age1wk - Age4wk
## 118 0.46988040   118 0.48072713 Age1wk - Age4wk
## 119 0.11049181   119 0.11202792 Age1wk - Age4wk
## 120 1.00000000   120 1.00000000 Age1wk - Age4wk
## 121 0.28247570   121 0.27848344 Age1wk - Age4wk
## 122 0.14655859   122 0.15271260 Age1wk - Age4wk
## 123 0.39759682   123 0.39944487 Age1wk - Age4wk
## 124 0.50868900   124 0.50402522 Age1wk - Age4wk
## 125 0.88697410   125 0.88167879 Age1wk - Age4wk
## 126 0.47855135   126 0.48693653 Age1wk - Age4wk
## 127 0.50868900   127 0.50402522 Age1wk - Age4wk
## 128 0.27100713   128 0.26811722 Age1wk - Age4wk
## 129 0.10896454   129 0.11202792 Age1wk - Age4wk
## 130 0.15992503   130 0.16822190 Age1wk - Age4wk
## 131 1.00000000   131 1.00000000 Age1wk - Age4wk
## 132 1.00000000   132 0.99931583 Age1wk - Age4wk
## 133 0.48623993   133 0.49661215 Age1wk - Age4wk
## 134 1.00000000   134 1.00000000 Age1wk - Age4wk
## 135 0.97897741   135 0.96483454 Age1wk - Age4wk
## 136 0.71205691   136 0.71618951 Age1wk - Age4wk
## 137 1.00000000   137 1.00000000 Age1wk - Age4wk
## 138 1.00000000   138 1.00000000 Age1wk - Age4wk
## 139 1.00000000   139 1.00000000 Age1wk - Age4wk
## 140 0.62053583   140 0.62778821 Age1wk - Age4wk
## 141 0.08133870   141 0.07905304 Age1wk - Age4wk
## 142 0.51096852   142 0.50697928 Age1wk - Age4wk
## 143 0.22685997   143 0.22685819 Age1wk - Age4wk
## 144 0.35364868   144 0.34083824 Age1wk - Age4wk
## 145 1.00000000   145 1.00000000 Age1wk - Age4wk
## 146 1.00000000   146 1.00000000 Age1wk - Age4wk
## 147 0.38364913   147 0.37813244 Age1wk - Age4wk
## 148 0.11360353   148 0.11513626 Age1wk - Age4wk
## 149 0.90528029   149 0.90169697 Age1wk - Age4wk
## 150 0.12174161   150 0.13147874 Age1wk - Age4wk
## 151 0.98810771   151 0.97361450 Age1wk - Age4wk
## 152 0.36608189   152 0.35324242 Age1wk - Age4wk
## 153 0.11902829   153 0.12452590 Age1wk - Age4wk
## 154 0.59539854   154 0.59658531 Age1wk - Age4wk
## 155 0.08374855   155 0.08562298 Age1wk - Age4wk
## 156 0.88260405   156 0.87805860 Age1wk - Age4wk
## 157 0.11205963   157 0.11346595 Age1wk - Age4wk
## 158 0.14271443   158 0.14930921 Age1wk - Age4wk
## 159 0.67038909   159 0.67552707 Age1wk - Age4wk
## 160 0.29233415   160 0.28705279 Age1wk - Age4wk
## 161 1.00000000   161 1.00000000 Age1wk - Age4wk
## 162 0.27223633   162 0.27007189 Age1wk - Age4wk
## 163 1.00000000   163 1.00000000 Age1wk - Age4wk
## 164 0.93927185   164 0.92854620 Age1wk - Age4wk
## 165 1.00000000   165 1.00000000 Age1wk - Age4wk
## 166 0.50868900   166 0.50402522 Age1wk - Age4wk
## 167 0.71205691   167 0.71618951 Age1wk - Age4wk
## 168 1.00000000   168 1.00000000 Age1wk - Age4wk
## 169 0.82215891   169 0.81929420 Age1wk - Age4wk
## 170 1.00000000   170 1.00000000 Age1wk - Age4wk
## 171 0.89320361   171 0.88925334 Age1wk - Age4wk
## 172 0.38364913   172 0.37898401 Age1wk - Age4wk
## 173 0.36697427   173 0.35447289 Age1wk - Age4wk
## 174 0.14270688   174 0.14930921 Age1wk - Age4wk
## 175 1.00000000   175 1.00000000 Age1wk - Age4wk
## 176 0.07424195   176 0.06870498 Age1wk - Age4wk
## 177 0.38364913   177 0.37813244 Age1wk - Age4wk
## 178 0.10896454   178 0.11139561 Age1wk - Age4wk
## 179 1.00000000   179 1.00000000 Age1wk - Age4wk
## 180 0.07424195   180 0.06870498 Age1wk - Age4wk
## 181 1.00000000   181 1.00000000 Age1wk - Age4wk
## 182 0.07424195   182 0.06870498 Age1wk - Age4wk
## 183 0.50868900   183 0.50402522 Age1wk - Age4wk
## 184 0.68078907   184 0.68223035 Age1wk - Age4wk
## 185 0.90112727   185 0.89441961 Age1wk - Age4wk
## 186 1.00000000   186 1.00000000 Age1wk - Age4wk
## 187 0.62078476   187 0.62778821 Age1wk - Age4wk
## 188 0.17885309   188 0.17889753 Age1wk - Age4wk
## 189 0.66020583   189 0.66516095 Age1wk - Age4wk
## 190 0.93927185   190 0.92854620 Age1wk - Age4wk
## 191 0.28462063   191 0.28024533 Age1wk - Age4wk
## 192 0.50868900   192 0.50402522 Age1wk - Age4wk
## 193 0.65404846   193 0.65990441 Age1wk - Age4wk
## 194 0.35364868   194 0.34083824 Age1wk - Age4wk
## 195 0.50868900   195 0.50612601 Age1wk - Age4wk
## 196 0.74194766   196 0.74331353 Age1wk - Age4wk
## 197 0.38626589   197 0.38338474 Age1wk - Age4wk
## 198 0.17885309   198 0.17889753 Age1wk - Age4wk
## 199 0.93927185   199 0.92854620 Age1wk - Age4wk
## 200 0.97897741   200 0.96483454 Age1wk - Age4wk
## 201 0.88241673   201 0.87805860 Age1wk - Age4wk
## 202 0.15067339   202 0.15710319 Age1wk - Age4wk
## 203 0.62269710   203 0.62851494 Age1wk - Age4wk
## 204 0.50868900   204 0.50402522 Age1wk - Age4wk
## 205 0.31371427   205 0.30956159 Age1wk - Age4wk
## 206 0.11205963   206 0.11346595 Age1wk - Age4wk
## 207 0.51708569   207 0.51354944 Age1wk - Age4wk
## 208 1.00000000   208 1.00000000 Age1wk - Age4wk
## 209 0.50868900   209 0.50402522 Age1wk - Age4wk
## 210 0.30486431   210 0.30113602 Age1wk - Age4wk
## 211 1.00000000   211 1.00000000 Age1wk - Age4wk
## 212 0.22228906   212 0.22155574 Age1wk - Age4wk
## 213 1.00000000   213 0.98471886 Age1wk - Age4wk
## 214 1.00000000   214 1.00000000 Age1wk - Age4wk
## 215 0.12174161   215 0.13126650 Age1wk - Age4wk
## 216 0.35364868   216 0.34083824 Age1wk - Age4wk
## 217 0.95164745   217 0.93882627 Age1wk - Age4wk
## 218 0.87489909   218 0.87023973 Age1wk - Age4wk
## 219 1.00000000   219 1.00000000 Age1wk - Age4wk
## 220 0.50868900   220 0.50402522 Age1wk - Age4wk
## 221 1.00000000   221 1.00000000 Age1wk - Age4wk
## 222 1.00000000   222 1.00000000 Age1wk - Age4wk
## 223 0.35364868   223 0.34083824 Age1wk - Age4wk
## 224 0.90609662   224 0.90626431 Age1wk - Age4wk
## 225 1.00000000   225 1.00000000 Age1wk - Age4wk
## 226 0.22228906   226 0.22155574 Age1wk - Age4wk
## 227 0.90110269   227 0.89441961 Age1wk - Age4wk
## 228 0.36697427   228 0.35447289 Age1wk - Age4wk
## 229 0.14271443   229 0.14930921 Age1wk - Age4wk
## 230 1.00000000   230 1.00000000 Age1wk - Age4wk
## 231 1.00000000   231 1.00000000 Age1wk - Age4wk
## 232 0.69014985   232 0.69528083 Age1wk - Age4wk
## 233 0.07424195   233 0.06870498 Age1wk - Age4wk
## 234 0.28247570   234 0.27930144 Age1wk - Age4wk
## 235 0.60829219   235 0.61452470 Age1wk - Age4wk
## 236 0.36608189   236 0.35324242 Age1wk - Age4wk
## 237 0.89466129   237 0.88925334 Age1wk - Age4wk
## 238 0.14271443   238 0.14930921 Age1wk - Age4wk
## 239 1.00000000   239 1.00000000 Age1wk - Age4wk
## 240 1.00000000   240 1.00000000 Age1wk - Age4wk
## 241 1.00000000   241 1.00000000 Age1wk - Age4wk
## 242 0.36608189   242 0.35324242 Age1wk - Age4wk
## 243 0.07424195   243 0.06870498 Age1wk - Age4wk
## 244 0.29199909   244 0.28705279 Age1wk - Age4wk
## 245 0.86877790   245 0.86295455 Age1wk - Age4wk
## 246 0.50868900   246 0.50402522 Age1wk - Age4wk
## 247 1.00000000   247 1.00000000 Age1wk - Age4wk
## 248 0.07424195   248 0.06870498 Age1wk - Age4wk
## 249 0.22658167   249 0.22537347 Age1wk - Age4wk
## 250 1.00000000   250 1.00000000 Age1wk - Age4wk
## 251 0.07424195   251 0.06870498 Age1wk - Age4wk
## 252 1.00000000   252 1.00000000 Age1wk - Age4wk
## 253 1.00000000   253 1.00000000 Age1wk - Age4wk
## 254 0.50868900   254 0.50402522 Age1wk - Age4wk
## 255 0.41804487   255 0.42512725 Age1wk - Age4wk
## 256 1.00000000   256 1.00000000 Age1wk - Age4wk
## 257 0.98028368   257 0.96500713 Age1wk - Age4wk
## 258 0.08133870   258 0.08392133 Age1wk - Age4wk
## 259 0.96194417   259 0.95048927 Age1wk - Age4wk
## 260 0.17885309   260 0.17889753 Age1wk - Age4wk
## 261 0.43173282   261 0.43706579 Age1wk - Age4wk
## 262 0.36697427   262 0.35447289 Age1wk - Age4wk
## 263 0.95164745   263 0.94002750 Age1wk - Age4wk
## 264 0.52670748   264 0.52299681 Age1wk - Age4wk
## 265 0.18191558   265 0.18085154 Age1wk - Age4wk
## 266 0.50868900   266 0.50697928 Age1wk - Age4wk
## 267 1.00000000   267 1.00000000 Age1wk - Age4wk
## 268 0.50868900   268 0.50402522 Age1wk - Age4wk
## 269 0.60799002   269 0.61254059 Age1wk - Age4wk
## 270 1.00000000   270 0.98471886 Age1wk - Age4wk
## 271 0.13790108   271 0.14930921 Age1wk - Age4wk
## 272 0.25666111   272 0.25663070 Age1wk - Age4wk
## 273 0.42013126   273 0.42590436 Age1wk - Age4wk
## 274 0.28583808   274 0.28179301 Age1wk - Age4wk
## 275 0.29233415   275 0.28705279 Age1wk - Age4wk
## 276 0.22228906   276 0.22155574 Age1wk - Age4wk
## 277 0.22228906   277 0.22155574 Age1wk - Age4wk
## 278 0.50868900   278 0.50697928 Age1wk - Age4wk
## 279 0.80673963   279 0.80811918 Age1wk - Age4wk
## 280 1.00000000   280 1.00000000 Age1wk - Age4wk
## 281 0.08133870   281 0.08392133 Age1wk - Age4wk
## 282 1.00000000   282 1.00000000 Age1wk - Age4wk
## 283 1.00000000   283 1.00000000 Age1wk - Age4wk
## 284 0.36608189   284 0.35324242 Age1wk - Age4wk
## 285 0.19661120   285 0.19302778 Age1wk - Age4wk
## 286 0.90609662   286 0.90613228 Age1wk - Age4wk
## 287 0.90457443   287 0.89893083 Age1wk - Age4wk
## 288 1.00000000   288 1.00000000 Age1wk - Age4wk
## 289 1.00000000   289 1.00000000 Age1wk - Age4wk
## 290 0.36697427   290 0.35447289 Age1wk - Age4wk
## 291 1.00000000   291 1.00000000 Age1wk - Age4wk
## 292 0.45782345   292 0.46923166 Age1wk - Age4wk
## 293 0.50868900   293 0.50402522 Age1wk - Age4wk
## 294 0.50868900   294 0.50697928 Age1wk - Age4wk
## 295 1.00000000   295 1.00000000 Age1wk - Age4wk
## 296 0.88241673   296 0.87805860 Age1wk - Age4wk
## 297 0.07694118   297 0.07219674 Age1wk - Age4wk
## 298 0.88423333   298 0.87805860 Age1wk - Age4wk
## 299 0.26727963   299 0.26358473 Age1wk - Age4wk
## 300 0.49260314   300 0.50402522 Age1wk - Age4wk
## 301 0.88241673   301 0.87805860 Age1wk - Age4wk
## 302 0.50868900   302 0.50444565 Age1wk - Age4wk
## 303 0.56242832   303 0.56118631 Age1wk - Age4wk
## 304 0.92690999   304 0.92854620 Age1wk - Age4wk
## 305 0.89558731   305 0.89138603 Age1wk - Age4wk
## 306 0.11731936   306 0.11991309 Age1wk - Age4wk
## 307 1.00000000   307 1.00000000 Age1wk - Age4wk
## 308 1.00000000   308 1.00000000 Age1wk - Age4wk
## 309 0.89466129   309 0.88925334 Age1wk - Age4wk
## 310 1.00000000   310 1.00000000 Age1wk - Age4wk
## 311 0.17089437   311 0.17889753 Age1wk - Age4wk
## 312 0.95114957   312 0.93882627 Age1wk - Age4wk
## 313 0.22140172   313 0.22155574 Age1wk - Age4wk
## 314 0.89320361   314 0.88925334 Age1wk - Age4wk
## 315 0.95114957   315 0.93882627 Age1wk - Age4wk
## 316 0.08133870   316 0.08392133 Age1wk - Age4wk
## 317 1.00000000   317 1.00000000 Age1wk - Age4wk
## 318 0.07424195   318 0.06870498 Age1wk - Age4wk
## 319 0.45772838   319 0.46810870 Age1wk - Age4wk
## 320 0.77528100   320 0.77495059 Age1wk - Age4wk
## 321 1.00000000   321 1.00000000 Age1wk - Age4wk
## 322 1.00000000   322 1.00000000 Age1wk - Age4wk
## 323 0.37978534   323 0.36881269 Age1wk - Age4wk
## 324 0.91689643   324 0.91844991 Age1wk - Age4wk
## 325 0.38364913   325 0.37813244 Age1wk - Age4wk
## 326 0.22140172   326 0.22155574 Age1wk - Age4wk
## 327 1.00000000   327 1.00000000 Age1wk - Age4wk
## 328 0.11902829   328 0.12452590 Age1wk - Age4wk
## 329 0.82215891   329 0.81929420 Age1wk - Age4wk
## 330 0.43180365   330 0.43777937 Age1wk - Age4wk
## 331 0.67167002   331 0.67595323 Age1wk - Age4wk
## 332 0.95114957   332 0.93882627 Age1wk - Age4wk
## 333 0.36608189   333 0.35318631 Age1wk - Age4wk
## 334 0.71490202   334 0.71651981 Age1wk - Age4wk
## 335 0.52670748   335 0.52299681 Age1wk - Age4wk
## 336 0.15750735   336 0.16607809 Age1wk - Age4wk
## 337 1.00000000   337 1.00000000 Age1wk - Age4wk
## 338 0.32672678   338 0.31652868 Age1wk - Age4wk
## 339 0.15750735   339 0.16607809 Age1wk - Age4wk
## 340 0.49260314   340 0.50402522 Age1wk - Age4wk
## 341 0.23319278   341 0.23400689 Age1wk - Age4wk
## 342 0.97897741   342 0.96483454 Age1wk - Age4wk
## 343 0.50868900   343 0.50402522 Age1wk - Age4wk
## 344 0.71490202   344 0.71651981 Age1wk - Age4wk
## 345 0.50868900   345 0.50402522 Age1wk - Age4wk
##     PValue_adj_withinNhood
## 1             0.4850611329
## 2             0.1449813962
## 3             0.5958829418
## 4             0.0429890352
## 5             0.0212702168
## 6             0.1139488410
## 7             0.3238792907
## 8             0.1530877495
## 9             0.9841738976
## 10            0.0044186929
## 11            0.9069024878
## 12            0.2842328324
## 13            0.2572220424
## 14            0.5307865730
## 15            0.2950678547
## 16            1.0000000000
## 17            0.7995833597
## 18            0.2467555115
## 19            0.1563124305
## 20            0.0400970510
## 21            0.0110403050
## 22            0.2409764063
## 23            0.3922087813
## 24            0.0152890694
## 25            0.0389286509
## 26            0.0205265195
## 27            0.2057745727
## 28            0.4700030900
## 29            0.5848030831
## 30            0.9565854380
## 31            0.1651790616
## 32            0.5540032980
## 33            0.4541299330
## 34            0.2682850402
## 35            0.5631021139
## 36            0.1170062904
## 37            0.0986083837
## 38            0.5212813073
## 39            0.1467362590
## 40            0.5751149500
## 41            0.2494321188
## 42            0.6088552483
## 43            0.2591459898
## 44            0.8498421703
## 45            0.0035709546
## 46            0.0293144552
## 47            1.0000000000
## 48            0.2409764078
## 49            0.2508526933
## 50            0.8715943487
## 51            0.0176221369
## 52            0.1431224460
## 53            0.3965369305
## 54            0.6573129098
## 55            0.9867570025
## 56            0.2409764103
## 57            0.5774588540
## 58            0.1915638082
## 59            0.6128687161
## 60            0.9400380380
## 61            0.9829060358
## 62            0.1405994542
## 63            0.5857200898
## 64            0.1065145814
## 65            0.0043300806
## 66            1.0000000000
## 67            0.6915218824
## 68            0.0127034726
## 69            0.0285061004
## 70            0.4666741338
## 71            0.2493440054
## 72            0.0473446891
## 73            0.0028528939
## 74            0.4839915537
## 75            1.0000000000
## 76            0.0075223258
## 77            1.0000000000
## 78            0.1294035773
## 79            0.0689605771
## 80            0.0528909996
## 81            0.1311665641
## 82            0.2571302364
## 83            0.7491305370
## 84            0.0042708590
## 85            1.0000000000
## 86            0.1158842143
## 87            1.0000000000
## 88            0.9788789831
## 89            1.0000000000
## 90            0.0410237980
## 91            0.3060852990
## 92            0.6391942133
## 93            0.1403931487
## 94            0.7825580168
## 95            0.2413169209
## 96            0.0191163382
## 97            0.0701733070
## 98            0.8748280008
## 99            0.0016080060
## 100           0.3330727919
## 101           0.1273686104
## 102           0.0114927245
## 103           0.2492049891
## 104           0.1792019824
## 105           1.0000000000
## 106           1.0000000000
## 107           0.1485948292
## 108           0.9403737342
## 109           0.0856876040
## 110           0.5124180903
## 111           0.1166180759
## 112           0.1804378554
## 113           0.0075801416
## 114           0.8587468293
## 115           0.9321837993
## 116           0.2052935815
## 117           0.8130559691
## 118           0.1879521610
## 119           0.0080066531
## 120           1.0000000000
## 121           0.0647004127
## 122           0.0187720218
## 123           0.1393081611
## 124           0.2246742265
## 125           0.5990288826
## 126           0.1941947508
## 127           0.2244517583
## 128           0.0604856499
## 129           0.0071856010
## 130           0.0236410907
## 131           1.0000000000
## 132           0.8000192392
## 133           0.1987241465
## 134           1.0000000000
## 135           0.7489977090
## 136           0.4189784128
## 137           1.0000000000
## 138           1.0000000000
## 139           0.9720149076
## 140           0.3435430274
## 141           0.0029779565
## 142           0.2621490683
## 143           0.0473210512
## 144           0.0967870326
## 145           1.0000000000
## 146           0.8100682659
## 147           0.1296992633
## 148           0.0092199968
## 149           0.6428802028
## 150           0.0123617711
## 151           0.7618453635
## 152           0.1059736593
## 153           0.0109202758
## 154           0.3209974721
## 155           0.0048549883
## 156           0.5884026980
## 157           0.0084607404
## 158           0.0174435850
## 159           0.3808587272
## 160           0.0733525423
## 161           1.0000000000
## 162           0.0615490827
## 163           0.9484345694
## 164           0.6839111355
## 165           1.0000000000
## 166           0.2159050463
## 167           0.4187230121
## 168           0.9607378208
## 169           0.5147429673
## 170           1.0000000000
## 171           0.6135920462
## 172           0.1312191234
## 173           0.1139087425
## 174           0.0161320823
## 175           1.0000000000
## 176           0.0008703279
## 177           0.1298392078
## 178           0.0066483491
## 179           1.0000000000
## 180           0.0014307364
## 181           1.0000000000
## 182           0.0012305354
## 183           0.2409764103
## 184           0.3926870259
## 185           0.6320950688
## 186           1.0000000000
## 187           0.3454802153
## 188           0.0294532578
## 189           0.3731598196
## 190           0.6911066527
## 191           0.0668239729
## 192           0.2423250385
## 193           0.3677837735
## 194           0.0972697908
## 195           0.2523882369
## 196           0.4430180246
## 197           0.1332337422
## 198           0.0283475510
## 199           0.6882916365
## 200           0.7446707638
## 201           0.5760377163
## 202           0.0204163551
## 203           0.3483493933
## 204           0.2288735246
## 205           0.0809291884
## 206           0.0087698840
## 207           0.2671604337
## 208           0.9427998597
## 209           0.2406286738
## 210           0.0777624918
## 211           0.9765753039
## 212           0.0441341204
## 213           0.7773748831
## 214           1.0000000000
## 215           0.0120486934
## 216           0.0961669865
## 217           0.7117482350
## 218           0.5604426076
## 219           1.0000000000
## 220           0.2409764063
## 221           1.0000000000
## 222           1.0000000000
## 223           0.0973815214
## 224           0.6487126537
## 225           1.0000000000
## 226           0.0440695793
## 227           0.6294659395
## 228           0.1104987700
## 229           0.0165797539
## 230           1.0000000000
## 231           1.0000000000
## 232           0.4020873010
## 233           0.0019367466
## 234           0.0655016108
## 235           0.3350014933
## 236           0.1063357997
## 237           0.6191477633
## 238           0.0177875957
## 239           1.0000000000
## 240           1.0000000000
## 241           1.0000000000
## 242           0.1079024396
## 243           0.0011624817
## 244           0.0719418044
## 245           0.5533295806
## 246           0.2409764066
## 247           1.0000000000
## 248           0.0018897394
## 249           0.0459730926
## 250           0.9697298402
## 251           0.0018409917
## 252           1.0000000000
## 253           0.8244064352
## 254           0.2409764063
## 255           0.1561129102
## 256           1.0000000000
## 257           0.7529715254
## 258           0.0040165257
## 259           0.7249434317
## 260           0.0295496405
## 261           0.1651847330
## 262           0.1169859271
## 263           0.7144251839
## 264           0.2757291011
## 265           0.0305829093
## 266           0.2568539763
## 267           0.9960808628
## 268           0.2409764103
## 269           0.3327466855
## 270           0.7800751321
## 271           0.0147893908
## 272           0.0557958925
## 273           0.1583103287
## 274           0.0679383262
## 275           0.0737190462
## 276           0.0444578126
## 277           0.0438221774
## 278           0.2580989043
## 279           0.4980740300
## 280           0.9461298746
## 281           0.0040588446
## 282           1.0000000000
## 283           1.0000000000
## 284           0.1082329070
## 285           0.0336233648
## 286           0.6474664067
## 287           0.6397569896
## 288           0.8220299732
## 289           1.0000000000
## 290           0.1109865315
## 291           1.0000000000
## 292           0.1818023570
## 293           0.2409764078
## 294           0.2595051148
## 295           1.0000000000
## 296           0.5836816856
## 297           0.0022301791
## 298           0.5920518829
## 299           0.0588789905
## 300           0.2070361013
## 301           0.5828740851
## 302           0.2478524384
## 303           0.2999617703
## 304           0.6716739074
## 305           0.6230172612
## 306           0.0098616274
## 307           0.9552953611
## 308           1.0000000000
## 309           0.6197798520
## 310           1.0000000000
## 311           0.0257579926
## 312           0.7030642081
## 313           0.0410716226
## 314           0.6079124071
## 315           0.7085375063
## 316           0.0044795224
## 317           1.0000000000
## 318           0.0010021747
## 319           0.1794162881
## 320           0.4719101768
## 321           1.0000000000
## 322           1.0000000000
## 323           0.1221918056
## 324           0.6617600301
## 325           0.1298856340
## 326           0.0403367412
## 327           0.9717472193
## 328           0.0107254131
## 329           0.5141147601
## 330           0.1664634365
## 331           0.3835333149
## 332           0.7065664804
## 333           0.1035783955
## 334           0.4236719993
## 335           0.2763305905
## 336           0.0224068729
## 337           1.0000000000
## 338           0.0861801072
## 339           0.0228271528
## 340           0.2038752502
## 341           0.0493422408
## 342           0.7406630218
## 343           0.2342139277
## 344           0.4247968539
## 345           0.2409764063
## 
## $design_df
##        Sample  Age
## 1_1wk   1_1wk  1wk
## 1_4wk   1_4wk  4wk
## 1_16wk 1_16wk 16wk
## 1_32wk 1_32wk 32wk
## 1_52wk 1_52wk 52wk
## 2_32wk 2_32wk 32wk
## 2_4wk   2_4wk  4wk
## 2_1wk   2_1wk  1wk
## 2_16wk 2_16wk 16wk
## 2_52wk 2_52wk 52wk
## 3_4wk   3_4wk  4wk
## 3_1wk   3_1wk  1wk
## 3_52wk 3_52wk 52wk
## 3_16wk 3_16wk 16wk
## 3_32wk 3_32wk 32wk
## 4_1wk   4_1wk  1wk
## 4_16wk 4_16wk 16wk
## 4_4wk   4_4wk  4wk
## 4_32wk 4_32wk 32wk
## 4_52wk 4_52wk 52wk
## 5_32wk 5_32wk 32wk
## 5_52wk 5_52wk 52wk
## 5_1wk   5_1wk  1wk
## 5_4wk   5_4wk  4wk
## 5_16wk 5_16wk 16wk
## 
## $formula
## [1] "~0 + Age"
## 
## $contrasts
## [1] "Age1wk - Age4wk"
## 
## $contrasts_model
## [1] "Age1wk - Age4wk"

22.3 Multi-contrast testing

Use per_contrast = FALSE to fit one model and test multiple contrasts jointly. Use per_contrast = TRUE to run each contrast and stack results.

contrasts <- c(
  "Age1wk - Age4wk",
  "Age4wk - Age16wk",
  "Age16wk - Age32wk",
  "Age32wk - Age52wk"
)

res2 <- RunMilo(
  sce = sce,
  sample_col = "Sample",
  condition_col = "Age",
  name = "milo_multi",
  contrasts = contrasts,
  per_contrast = TRUE,
  k1 = 11, k2 = 11, d1 = 40, d2 = 40, d3 = 40,
  prop = 0.2,
  refinement_scheme = "graph"
)

head(res2$da_results)

##        logFC   logCPM         F     PValue       FDR Nhood
## 1  0.8854248 13.75617 0.4875157 0.48506113 0.7893684     1
## 2 -2.0182655 13.53681 2.1247557 0.14498140 0.4033757     2
## 3 -0.6804019 13.51842 0.2812763 0.59588294 0.8861190     3
## 4 -2.7945200 13.62681 4.0973461 0.04298904 0.2222891     4
## 5 -3.2774410 13.71092 5.3069395 0.02127022 0.1528797     5
## 6 -2.2143078 13.67219 2.4992158 0.11394884 0.3669743     6
##   SpatialFDR        contrast PValue_adj_withinNhood
## 1  0.7884234 Age1wk - Age4wk             0.96139701
## 2  0.4027576 Age1wk - Age4wk             0.57992558
## 3  0.8790454 Age1wk - Age4wk             0.59588294
## 4  0.2215557 Age1wk - Age4wk             0.17195614
## 5  0.1607883 Age1wk - Age4wk             0.08508087
## 6  0.3544729 Age1wk - Age4wk             0.45579536

22.4 GLMM (random intercept)

When samples are not independent (e.g., repeated measures), a random intercept can help control correlation structure.

suppressMessages(library(scRNAseq))
suppressMessages(library(scater))
suppressMessages(library(scran))
suppressMessages(library(scuttle))
conflicted::conflicts_prefer(base::intersect, .quiet = TRUE)
library(sclet)

sce2 <- KotliarovPBMCData(mode = "rna", ensembl = FALSE)
colData(sce2)$ObsID <- paste(colData(sce2)$tenx_lane, colData(sce2)$sampleid, sep = "_")

set.seed(42)
keep_samps <- sample(unique(colData(sce2)$ObsID), size = 40)
sce2 <- sce2[, colData(sce2)$ObsID %in% keep_samps]

sce2 <- NormalizeData(sce2)
sce2 <- RunPCA(sce2, ncomponents = 30)
sce2 <- RunUMAP(sce2, dims = 1:30)

res3 <- RunMilo(
  sce = sce2,
  sample_col = "ObsID",
  condition_col = "adjmfc.time",
  name = "milo_glmm",
  contrasts = c("adjmfc.timed0 high"),
  glmm = TRUE,
  random_effect = "tenx_lane",
  k1 = 60, k2 = 60, d1 = 30, d2 = 30, d3 = 30,
  prop = 0.05,
  overlap = 25
)

head(res3$da_results)

##         logFC   logCPM        SE     tvalue       PValue
## 1  1.19703375 10.82839 0.3291211  3.6370617 0.0002781796
## 2 -0.56029080 10.29788 0.3573607 -1.5678581 0.1169667207
## 3 -0.02648526 11.70938 0.3682585 -0.0719203 0.9426680337
## 4 -1.38022884 10.50019 0.4339954 -3.1802848 0.0014743506
## 5  0.04655340 10.61860 0.3087125  0.1507986 0.8801388359
## 6  0.36956464 11.77586 0.3560930  1.0378319 0.2993804523
##   tenx_lane_variance Converged Logliklihood Nhood
## 1         0.00000001      TRUE     336.7509     1
## 2         0.01364852     FALSE     200.6110     2
## 3         0.00000001      TRUE     850.5483     3
## 4         1.12593495      TRUE     242.7716     4
## 5         0.00000001      TRUE     238.2296     5
## 6         0.08523814     FALSE     776.3678     6
##    SpatialFDR           contrast PValue_adj_withinNhood
## 1 0.002192376 adjmfc.timed0 high           0.0002781796
## 2 0.265778252 adjmfc.timed0 high           0.1169667207
## 3 0.967250639 adjmfc.timed0 high           0.9426680337
## 4 0.009966656 adjmfc.timed0 high           0.0014743506
## 5 0.928078893 adjmfc.timed0 high           0.8801388359
## 6 0.468519021 adjmfc.timed0 high           0.2993804523

22.5 Refit after dropping separated neighbourhoods

In GLMM mode, some neighbourhoods can show perfect separation and return unstable estimates. You can diagnose with miloR::checkSeparation() and refit after dropping those neighbourhoods.

If you keep multiple Milo runs in the same object, give them different name values and inspect a specific record with get_milo(sce, id = "your_id").

milo_info <- get_milo(res3$sce)
design_df <- milo_info$design_df

bad_hood <- which(miloR::checkSeparation(
  res3$milo,
  design.df = design_df,
  condition = "adjmfc.time",
  min.val = 10
))

refit <- refit_milo(
  milo = res3$milo,
  design_df = design_df,
  bad_hood = bad_hood,
  formula = milo_info$formula,
  contrasts = milo_info$contrasts,
  glmm = TRUE,
  old_results = res3$da_results
)

head(refit$da_clean)

##         logFC   logCPM        SE      tvalue      PValue
## 1  1.19701778 10.82839 0.3325076  3.59997128 0.000320980
## 2 -0.55973508 10.29788 0.3560395 -1.57211518 0.115974505
## 3 -0.02647832 11.70938 0.3687434 -0.07180689 0.942758290
## 4 -1.38234653 10.50019 0.4317662 -3.20160925 0.001369448
## 5  0.04655352 10.61860 0.3087126  0.15079892 0.880138552
## 6  0.35785432 11.77586 0.3539698  1.01097426 0.312062809
##   tenx_lane_variance Converged Logliklihood Nhood
## 1         0.00000001      TRUE     336.9308     1
## 2         0.01748438     FALSE     200.8450     2
## 3         0.00000001      TRUE     850.5466     3
## 4         1.13627082      TRUE     243.0364     4
## 5         0.00000001      TRUE     238.2296     5
## 6         0.08938493      TRUE     776.0518     6
##    SpatialFDR
## 1 0.002488719
## 2 0.261422660
## 3 0.967049762
## 4 0.009281803
## 5 0.927874576
## 6 0.485190403